[galaxy-dev] Re: Upgrade galaxy built from source?

[Dannon Baker]

This depends a bit on the installation, but general procedures (a bit
dated, but these still apply) can be found here:
https://galaxyproject.org/admin/maintenance/

Ideally, without any local code customizations, it's really just something
like:
```
git fetch origin
git checkout release_20.09 && git pull --ff-only origin release_20.09
sh manage_db.sh upgrade
sh run.sh
```


On Tue, Sep 22, 2020 at 7:45 PM Sandra Maksimovic <
sandra.maksimo...@mcri.edu.au> wrote:

> Hi there,
>
> Does anyone know of a best practice method to upgrade a Galaxy instance
> built from source?
>
> Thanks,
> Sandra
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[galaxy-dev] Re: King Skrupellos hack

[Dannon Baker]

Sorry for the delayed response here, I think this fell through the cracks
while folks were engaged with GCC this year.  The attachment didn't make it
through, can you provide more information?  For what it's worth, we've seen
'hacks' like this in the past simply be that someone uploads data with spam
text/links in the contents, so it may not be much to worry about.

On Thu, Jul 11, 2019 at 7:44 AM Pat Gillevet  wrote:

>
> Has anyone been hacked through the galaxy port 8080?  We have an aberrant
> link on our install and I cannot find where it is hidden.
>
> The message that comes up is attached.
>
> Pat
>
>
> 
> Patrick M. Gillevet, Ph.D
>Director, Microbiome Analysis Center
>   Professor, Department of Biology
> George Mason University, Science & Technology Campus
> 10900 University Boulevard, MSN 4D4
>  Manassas, Virginia  20110
> Office 703-993-1057 Room Colgan Hall-426 FAX 703-993-8430
>   http://mbac.gmu.edu
>
> **
>
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[galaxy-dev] Re: new datasets appear in database/files/000/

[Dannon Baker]

Hi Jochen,

Yes, those new directories would coincide with when you passed 100,000
datasets on your instance, so congrats!  You can see the code that builds
this hashed path here:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/__init__.py#L137

So, for example, dataset id `9` Will be in folder 'datasets/099/'.
Dataset '10' will be in 'datasets/000/100/'.

Sorry for the slow response, hope this clears up the storage path logic!

-Dannon

On Tue, May 21, 2019 at 11:38 AM Jochen Bick 
wrote:

> Coming back to my question:
>
> this is how an ls -ls looks in my database folder...
>
> 2. Apr 14:40 000/
> 9. Nov 2015 005/
> 19. Nov 2018 007/
> 19. Nov 2018 008/
> 3. Dez 2015 010/
> 10. Jan 2017 012/
> 10. Jan 2017 013/
> 29. Jun 2017 014/
> 4. Jul 2017 015/
> 9. Jan 2018 018/
> 29. Jun 2017 020/
> 21. Sep 2016 021/
> 20. Mär 2018 032/
> 29. Jan 09:38 033/
> 29. Jan 10:32 034/
> 16. Jul 2018 035/
> 30. Okt 2018 036/
> 30. Okt 2018 037/
> 30. Okt 2018 038/
> 30. Okt 2018 039/
> 29. Aug 2018 070/
> 29. Aug 2018 071/
> 29. Aug 2018 072/
> 29. Aug 2018 073/
> 29. Aug 2018 074/
> 29. Aug 2018 075/
> 29. Aug 2018 076/
> 29. Aug 2018 077/
> 29. Aug 2018 078/
> 29. Aug 2018 079/
> 29. Aug 2018 080/
> 29. Aug 2018 081/
> 29. Aug 2018 082/
> 29. Aug 2018 083/
> 29. Aug 2018 084/
> 29. Aug 2018 085/
> 29. Aug 2018 086/
> 29. Aug 2018 087/
> 29. Aug 2018 088/
> 29. Aug 2018 089/
> 29. Aug 2018 090/
> 29. Aug 2018 091/
> 29. Aug 2018 092/
> 29. Aug 2018 093/
> 29. Aug 2018 094/
> 29. Aug 2018 095/
> 31. Aug 2018 096/
> 30. Aug 2018 097/
> 1. Sep 2018 098/
> 24. Okt 2018 099/
>
>
> if you look into the 000 folder it restarts:
>
> 10. Dez 19:36 100/
> 30. Nov 10:45 101/
> 10. Dez 19:39 102/
> 10. Dez 19:37 103/
> 11. Jan 15:13 104/
> 11. Jan 11:31 105/
> 22. Jan 14:33 106/
> 8. Feb 10:46 107/
> 14. Feb 15:47 108/
> 21. Mär 11:00 109/
> 2. Apr 15:22 110/
> 21. Mai 17:17 111/
>
> is this the expected behavior?
>
> The only thing we did was we archived some of the very early generated
> datasets. Is this maybe the problem?
>
>
> Cheers Jochen
>
>
> On 14.05.19 15:32, Jochen Bick wrote:
> > Hi,
> >
> > today we found out that some of our files in your galaxy instance are
> > new in "database/files/000/" which is the first folder of your database
> > files. Could some please explain me how galaxy generates new file names?
> > and how this is possible?
> >
> > Thanks in advance Jochen
> >
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone +41 52 354 92 06
> jochen.b...@usys.ethz.ch 
> www.ap.ethz.ch
>
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Re: [galaxy-dev] run.sh problem

[Dannon Baker]

Thanks for the information.  I've seen this error before, but only when
using an external (and incompatible) nodejs.  It looks like, in your case,
it's correctly using .venv/bin/node that Galaxy will have installed.  Can
you check the version of that for me with `
/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node
--version`?  And is there another node/yarn available on the system?

It might also be useful information to see what happens when you try the
client build directly, both within the .venv and without, so, from the
Galaxy directory try a `make client`.  Save the output of that, and then
`source .venv/bin/activate`, and `make client` again.

-Dannon

On Tue, Jan 8, 2019 at 11:15 AM Matthias Bernt  wrote:

> Hi Dannon,
>
> We are trying to run release_18.09.
>
> Indeed the output was from planemo, but we get the same (yarn) error
> when ./run.sh is called without planemo:
>
> ```
> $ NODE_ENV=production gulp staging && concurrently "yarn run style"
> "yarn run webpack-production-maps" "yarn run gulp clean && yarn run
> gulp-production-maps" && yarn run save-build-hash
> gulp[14831]: ../src/node_contextify.cc:628:static void
> node::contextify::ContextifyScript::New(const
> v8::FunctionCallbackInfo&): Assertion `args[1]->IsString()'
> failed.
>   1: 0x8daaa0 node::Abort() [gulp]
>   2: 0x8dab75  [gulp]
>   3: 0x90e2f7
> node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo
> const&) [gulp]
>   4: 0xb5e71b  [gulp]
>   5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int,
> v8::internal::Object**, v8::internal::Isolate*) [gulp]
>   6: 0x2ce8440dbe1d
> /tmp/yarn--1546961268610-0.24122682361732672/node: line 3: 14831
> Aborted (core dumped)
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node"
> "$@"
> error Command failed with exit code 134.
> info Visit https://yarnpkg.com/en/docs/cli/run for documentation about
> this command.
> ERROR: Galaxy client build failed. See ./client/README.md for more
> information, including how to get help.
> ```
>
> Best,
> Matthias
>
>
> On 08.01.19 16:09, Dannon Baker wrote:
> > What version of Galaxy exactly is this?  And, it looks like it's being
> > run by planemo, and not a simple 'run.sh' via the command line -- is
> > that correct?
> >
> > On Tue, Jan 8, 2019 at 10:04 AM Matthias Bernt  > <mailto:m.be...@ufz.de>> wrote:
> >
> > Dear all,
> >
> > a colleague tries to run.sh on a Manjaro Linux and got the following
> > error:
> >
> >
> > ```
> > yarn run v1.12.3
> > $ NODE_ENV=production gulp staging && concurrently "yarn run style"
> > "yarn run webpack-production-maps" "yarn run gulp clean && yarn run
> > gulp-production-maps" && yarn run save-build-hash
> > gulp[12888]: ../src/node_contextify.cc:628:static void
> > node::contextify::ContextifyScript::New(const
> > v8::FunctionCallbackInfo&): Assertion
> `args[1]->IsString()'
> > failed.
> >1: 0x8daaa0 node::Abort() [gulp]
> >2: 0x8dab75  [gulp]
> >3: 0x90e2f7
> >
>  node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo
> > const&) [gulp]
> >4: 0xb5e71b  [gulp]
> >5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int,
> > v8::internal::Object**, v8::internal::Isolate*) [gulp]
> >6: 0x6f20bcdbe1d
> > /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888
> > Aborted (core dumped)
> >
>  "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node"
> > "$@"
> > error Command failed with exit code 134.
> > info Visit https://yarnpkg.com/en/docs/cli/run for documentation
> about
> > this command.
> > ERROR: Galaxy client build failed. See ./client/README.md for more
> > information, including how to get help.
> > Problem running Galaxy command [].
> > Traceback (most recent call last):
> > File
> >
>  
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo",
> > line 11, in 
> >   sys.exit(planemo())
> > File
> >
>  
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> > line 764, in __call__
> >   return self.main(*args, **kwargs)
> > File
> >

Re: [galaxy-dev] run.sh problem

[Dannon Baker]

What version of Galaxy exactly is this?  And, it looks like it's being run
by planemo, and not a simple 'run.sh' via the command line -- is that
correct?

On Tue, Jan 8, 2019 at 10:04 AM Matthias Bernt  wrote:

> Dear all,
>
> a colleague tries to run.sh on a Manjaro Linux and got the following error:
>
>
> ```
> yarn run v1.12.3
> $ NODE_ENV=production gulp staging && concurrently "yarn run style"
> "yarn run webpack-production-maps" "yarn run gulp clean && yarn run
> gulp-production-maps" && yarn run save-build-hash
> gulp[12888]: ../src/node_contextify.cc:628:static void
> node::contextify::ContextifyScript::New(const
> v8::FunctionCallbackInfo&): Assertion `args[1]->IsString()'
> failed.
>   1: 0x8daaa0 node::Abort() [gulp]
>   2: 0x8dab75  [gulp]
>   3: 0x90e2f7
> node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo
> const&) [gulp]
>   4: 0xb5e71b  [gulp]
>   5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int,
> v8::internal::Object**, v8::internal::Isolate*) [gulp]
>   6: 0x6f20bcdbe1d
> /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888
> Aborted (core dumped)
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node"
> "$@"
> error Command failed with exit code 134.
> info Visit https://yarnpkg.com/en/docs/cli/run for documentation about
> this command.
> ERROR: Galaxy client build failed. See ./client/README.md for more
> information, including how to get help.
> Problem running Galaxy command [].
> Traceback (most recent call last):
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo",
> line 11, in 
>  sys.exit(planemo())
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 764, in __call__
>  return self.main(*args, **kwargs)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 717, in main
>  rv = self.invoke(ctx)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 1137, in invoke
>  return _process_result(sub_ctx.command.invoke(sub_ctx))
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 956, in invoke
>  return ctx.invoke(self.callback, **ctx.params)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 555, in invoke
>  return callback(*args, **kwargs)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py",
> line 64, in new_func
>  return ctx.invoke(f, obj, *args, **kwargs)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py",
> line 555, in invoke
>  return callback(*args, **kwargs)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py",
> line 195, in handle_blended_options
>  return f(*args, **kwds)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py",
> line 43, in cli
>  galaxy_serve(ctx, runnables, **kwds)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py",
> line 22, in serve
>  return _serve(ctx, runnables, **kwds)
>File
>
> "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py",
> line 54, in _serve
>  raise Exception(message)
> Exception: Problem running Galaxy command [].
> ```
>
> Would be great to have a suggestion...
>
> Cheers,
> Matthias
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> ---
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[galaxy-dev] Galaxy 18.09 Release

[Dannon Baker]

We are pleased to announce the *release of Galaxy 18.09
*.
A few release highlights are:

Extensive Workflow Enhancements

Workflows got a lot of love this time around, with new runtime parameters
for subworkflows, exposed workflow versions, and zoom capability in the
editor, to name a few. There were also a number of usability enhancements
including better labeling, links, overhauled workflow import interfaces,
and many more.
 Group Tags

Galaxy now contains powerful new features for multiple factor analysis of
collections of datasets. The concept of group tags has been added to
Galaxy. These are a special class of tags that describe key-value pairs
that can be attached to the contents of a collection during upload or using
collection operation tools. These tags can describe multiple sets of
variables for the contents of a collection. Once set, these tags can be
consumed intelligently by tools that need to divide collections into
multiple overlapping factors or sets of datasets. A special thanks to
@mvdbeek for devising and implementing this approach.

Python 3 Beta Support

After almost 3 years of work and more than 100 pull requests, we are proud
to announce the Beta-stage support for running Galaxy under Python 3. Lint,
unit, API, framework, integration and Selenium tests all pass, time for you
to give it a try and report any bug you find!

Please see the full release notes

for more information, including how to upgrade today!

*Thanks for using Galaxy!*
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Re: [galaxy-dev] Update from 17.10 to 18.05

[Dannon Baker]

Can you look and see which resources are failing to load?  That'd help me
figure out what's going on here.  If you have any local changes to the
interface you will need to run 'make client-production' from the root of
the repository (which should be safe to do in any event, and will rebuild
the entire client application).

On Tue, Sep 18, 2018 at 7:48 AM Jochen Bick 
wrote:

> Hi,
>
> today we tried to update from 17.10 to 18.05
>
> your server is running but with out any interface, its just white after
> loading?
>
> 
> Galaxy
> | AP - Group
> 
> 
>  media="screen" rel="stylesheet" type="text/css" />
>  href="/static/style/jquery-ui/smoothness/jquery-ui.css?v=1537264325"
> media="screen" rel="stylesheet" type="text/css" />
>  rel="stylesheet" type="text/css" />
>  media="screen" rel="stylesheet" type="text/css" />
>
>
> # tail ./galaxy-dist/dsmerror.log
> 09/05/2018 11:18:21 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:18:22 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:19 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from
> lstat, errno = 6
> 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:40 ANS1999E Incremental processing of '/' stopped.
>
> Cheers Jochen
> ___
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Re: [galaxy-dev] MySQL errors and warnings with a fresh install of Galaxy 18-05

[Dannon Baker]

Frederic, you may want to follow this issue to track a resolution here:
https://github.com/galaxyproject/galaxy/issues/6401

On Thu, Jun 14, 2018 at 1:24 AM SAPET, Frederic 
wrote:

> Hi Hans,
>
> We have a very nice MySQL server with a lot of RAM and associated storage
> (as well as Oracle for some other applications)
> So we would like to avoid a third system to maintain.
> And mysql is working well for my current 17.09 galaxy instance.
>
> Fred
>
> -Message d'origine-
> De : Hans-Rudolf Hotz [mailto:h...@fmi.ch]
> Envoyé : jeudi 14 juin 2018 08:25
> À : SAPET, Frederic ; Galaxy-dev <
> galaxy-dev@lists.galaxyproject.org>
> Objet : Re: [galaxy-dev] MySQL errors and warnings with a fresh install of
> Galaxy 18-05
>
> Hi Fred
>
> Sorry, I don't have an answer I am just wondering: If you start from
> 'scratch', why don't you use PostgreSQL?
>
> Regards, Hans-Rudolf
>
>
>
> On 06/13/2018 05:41 PM, SAPET, Frederic wrote:
> > Hi,
> >
> > I try to install galaxy 18-05. My database backend is MysqL (5.7.11-4
> > Percona Server)
> >
> > I start from scratch (drop database, new directory with galaxy files
> > fetched with git)
> >
> > So the database is first created when run.sh is used : :
> >
> > Creating database for URI [mysql://….
> >
> > I see warnings about duplicated indexes and OperationalError from
> > SQLAlchemy.
> >
> > Some tables are then missing in my database
> > (workflow_invocation_output_dataset_collection_association and
> > workflow_invocation_output_dataset_collection_association).
> >
> > And fields are still present (ie in request table : library_id and
> > folder_id)
> >
> > Could you please help me ?
> >
> > Thank you.
> >
> > Fred
> >
> >>grep  "^OperationalError:" FirstRun.log  | cut -f 2- -d ","
> >
> > "Cannot drop index 'ix_request_library_id': needed in a foreign key
> > constraint") [SQL: u'\nALTER TABLE request DROP COLUMN library_id']
> > (Background on this error at: http://sqlalche.me/e/e3q8)
> >
> > "Cannot drop index 'ix_request_folder_id': needed in a foreign key
> > constraint") [SQL: u'\nALTER TABLE request DROP COLUMN folder_id']
> > (Background on this error at: http://sqlalche.me/e/e3q8)
> >
> > "BLOB/TEXT column 'annotation' used in key specification without a key
> > length") [SQL: u'CREATE INDEX
> > ix_page_annotation_association_annotation
> > ON page_annotation_association (annotation)'] (Background on this
> > error
> > at: http://sqlalche.me/e/e3q8)
> >
> > "Cannot drop index 'sequencer_id': needed in a foreign key
> > constraint")
> > [SQL: u'\nALTER TABLE request_type DROP COLUMN sequencer_id']
> > (Background on this error at: http://sqlalche.me/e/e3q8)
> >
> > "BLOB/TEXT column 'guid' used in key specification without a key
> > length") [SQL: u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON
> > tool_id_guid_map (guid)'] (Background on this error at:
> > http://sqlalche.me/e/e3q8)
> >
> > "BLOB/TEXT column 'layout' used in key specification without a key
> > length") [SQL: u'CREATE INDEX ix_form_definition_layout ON
> > form_definition (layout)'] (Background on this error at:
> > http://sqlalche.me/e/e3q8)
> >
> > "BLOB/TEXT column 'notification' used in key specification without a
> > key
> > length") [SQL: u'CREATE INDEX ix_request_notification ON request
> > (notification)'] (Background on this error at:
> > http://sqlalche.me/e/e3q8)
> >
> > "BLOB/TEXT column 'data_manager_id' used in key specification without
> > a key length") [SQL: u'CREATE INDEX
> > ix_data_manager_job_association_data_manager_id ON
> > data_manager_job_association (data_manager_id)'] (Background on this
> > error at: http://sqlalche.me/e/e3q8)
> >
> > "Identifier name
> > 'workflow_invocation_output_dataset_collection_association_ibfk_1' is
> > too long") [SQL: u'\nCREATE TABLE
> > workflow_invocation_output_dataset_collection_association (\n\tid
> > INTEGER NOT NULL AUTO_INCREMENT, \n\tworkflow_invocation_id INTEGER,
> > \n\tworkflow_step_id INTEGER, \n\tdataset_collection_id INTEGER,
> > \n\tworkflow_output_id INTEGER, \n\tPRIMARY KEY (id), \n\tFOREIGN
> > KEY(workflow_invocation_id) REFERENCES workflow_invocation (id),
> > \n\tFOREIGN KEY(workflow_step_id) REFERENCES workflow_step (id),
> > \n\tFOREIGN KEY(dataset_collection_id) REFERENCES
> > history_dataset_collection_association (id), \n\tFOREIGN
> > KEY(workflow_output_id) REFERENCES workflow_output (id)\n)\n\n']
> > (Background on this error at: http://sqlalche.me/e/e3q8)
> >
> > "Identifier name
> > 'workflow_invocation_step_output_dataset_collection_association_ibfk_1'
> > is too long") [SQL: u'\nCREATE TABLE
> > workflow_invocation_step_output_dataset_collection_association (\n\tid
> > INTEGER NOT NULL AUTO_INCREMENT, \n\tworkflow_invocation_step_id
> > INTEGER, \n\tworkflow_step_id INTEGER, \n\tdataset_collection_id
> > INTEGER, \n\toutput_name VARCHAR(255), \n\tPRIMARY KEY (id),
> > \n\tFOREIGN
> > KEY(workflow_invocation_step_id) REFERENCES workflow_invocation_step
> > (id), \n\tFOREIGN KEY(workflow_step_id)

Re: [galaxy-dev] tabular data display

[Dannon Baker]

Yeah, it was intentional to avoid browser crashes years ago with very large
tables.  50 was somewhat arbitrarily chosen, at the time.  We could make
this configurable for galaxy instances and/or increase it outright.  Here's
the logic in question, if you wanted to tinker with it:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabular.py#L90

On Fri, Jun 1, 2018 at 10:04 AM Matthias Bernt  wrote:

> Dear Dannon,
>
> its 59 columns :( the last columns are only sometimes 0.
>
> Is there a performance issue when rendering html tables with a larger
> number of columns?
>
> What would be the Galaxy way to handle data with a larger number of
> columns?
>
> I agree that the scidx problem is unrelated. Might be worth to open an
> issue?
>
> Best,
> Matthias
>
> On 01.06.2018 15:44, Dannon Baker wrote:
> > I'm not familiar with MetaProSIP, but how many columns *should* be in
> > the output?  Galaxy automatically displays tabular data with more than
> > 50 columns in the 'raw' view you're seeing here, instead of using a
> > table.  The last bit of data in particular, when looking at the sample,
> > is a ton of `0` columns.  Is that correct?
> >
> > One more possible issue is that this is sniffed as a `scidx` file, for
> > me, though that's unrelated to the display problem here.
> >
> > -Dannon
> >
> > On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt  > <mailto:m.be...@ufz.de>> wrote:
> >
> > Dear list,
> >
> > I'm struggling with tabular data in Galaxy. Attached is a tab
> separated
> > file that is generated by MetaProSIP (an updated - not yet committed
> --
> > version).
> >
> > The problem is that it is not shown as table in Galaxy (dev) at all.
> > Also the peek preview is odd, some values of the header and data are
> > omitted.
> >
> > Is this a bug in Galaxy, or of the data in the table?
> >
> > Cheers,
> > Matthias
> > --
> >
> > ---
> > Matthias Bernt
> > Bioinformatics Service
> > Molekulare Systembiologie (MOLSYB)
> > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> > Helmholtz Centre for Environmental Research GmbH - UFZ
> > Permoserstraße 15, 04318 Leipzig, Germany
> > Phone +49 341 235 482296,
> > m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <
> http://www.ufz.de>
> >
> > Sitz der Gesellschaft/Registered Office: Leipzig
> > Registergericht/Registration Office: Amtsgericht Leipzig
> > Handelsregister Nr./Trade Register Nr.: B 4703
> > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> > MinDirig Wilfried Kraus
> > Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> > Prof. Dr. Dr. h.c. Georg Teutsch
> > Administrative Geschäftsführerin/ Administrative Managing Director:
> > Prof. Dr. Heike Graßmann
> > ---
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> > https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> > http://galaxyproject.org/search/
> >
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
>
___
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Re: [galaxy-dev] tabular data display

[Dannon Baker]

I'm not familiar with MetaProSIP, but how many columns *should* be in the
output?  Galaxy automatically displays tabular data with more than 50
columns in the 'raw' view you're seeing here, instead of using a table.
The last bit of data in particular, when looking at the sample, is a ton of
`0` columns.  Is that correct?

One more possible issue is that this is sniffed as a `scidx` file, for me,
though that's unrelated to the display problem here.

-Dannon

On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt  wrote:

> Dear list,
>
> I'm struggling with tabular data in Galaxy. Attached is a tab separated
> file that is generated by MetaProSIP (an updated - not yet committed --
> version).
>
> The problem is that it is not shown as table in Galaxy (dev) at all.
> Also the peek preview is odd, some values of the header and data are
> omitted.
>
> Is this a bug in Galaxy, or of the data in the table?
>
> Cheers,
> Matthias
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
___
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Re: [galaxy-dev] Trackster ownership issue

[Dannon Baker]

Ok, good to know what happened here, and that it's not a bug -- scared me a
bit at first, because this sort of access would *definitely* be
unintentional :)

-Dannon

On Wed, May 16, 2018 at 10:16 AM Previti <
christopher.prev...@dkfz-heidelberg.de> wrote:

> Ah, no I was wrong, they don't have the same email, they each have a
> separate account , i.e. cour...@dkfz.de, cour...@dkfz.de etc...
>
> The issue is that I set it up so all files associated with these accounts
> (everything in the histories) are stored in the same directory.
>
> That's why they could see each other's files in trackster, so it's not
> really an issue.
>
> Thanks for answering! This is the first time I did a Galaxy Course and I'm
> still optimizing a bit
>
> Christopher
>
> On 05/16/2018 03:55 PM, Dannon Baker wrote:
>
> Oh that's interesting.  It shouldn't be allowed to create multiple users
> with the same email address, unless you've changed that -- can you
> elaborate on what you've done?
>
> -Dannon
>
> On Wed, May 16, 2018 at 9:48 AM Previti <
> christopher.prev...@dkfz-heidelberg.de> wrote:
>
>> Hi,
>>
>> I just implemented a couple of features (impersonate/delete users) that
>> I'm going to use for troubleshooting due to the fact that this might be an
>> issue that is specific to us.
>>
>> I think it might be an issue with the user-accounts themselves...they're
>> "artificial" in a sense that they are called "course1" through "course10"
>> (as username and password) and all associated with the same email address...
>>
>> Could this be problematic in general?
>> Cheers,
>> Christopher
>>
>> On 05/16/2018 02:35 PM, Dannon Baker wrote:
>>
>> I definitely have not seen this before, and am not able to reproduce it
>> on my local instance.  Can you provide a screenshot of what you're seeing,
>> and the organization of the histories that are being sourced for the
>> incorrect datasets?
>>
>> On Wed, May 16, 2018 at 7:25 AM Previti <
>> christopher.prev...@dkfz-heidelberg.de> wrote:
>>
>>> Dear all,
>>>
>>> I'm having a strange issue with Trackster in our Galaxy implementation.
>>>
>>> Users seem to be able to upload files ("Add Datasets") from* all *histories
>>> of all users, regardless of ownership.
>>>
>>> ...is this something that has been observed before...? How do I stop
>>> this from happening?
>>>
>>> Thanks and best regards,
>>>
>>> Christopher
>>> --
>>> *Dr. Christopher Previti*
>>> Genomics and Proteomics Core Facility
>>> High Throughput Sequencing (W190)
>>> Bioinformatician
>>>
>>> German Cancer Research Center (DKFZ)
>>> Foundation under Public Law
>>> Im Neuenheimer Feld 580
>>> 69120 Heidelberg
>>> Germany
>>> Room: B2.102 (INF580/TP3)
>>> Phone: +49 6221 42-4661
>>>
>>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>>> www.dkfz.de
>>>
>>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>>> VAT-ID No.: DE143293537
>>>
>>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
>>> Personen bestimmt, an die sie adressiert ist.
>>> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
>>> Informationen enthalten. Sollten Sie nicht
>>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
>>> Absender und löschen Sie die Mitteilung.
>>> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
>>> untersagt.
>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/
>>
>>
>> --
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4661
>>
>>

Re: [galaxy-dev] Trackster ownership issue

[Dannon Baker]

Oh that's interesting.  It shouldn't be allowed to create multiple users
with the same email address, unless you've changed that -- can you
elaborate on what you've done?

-Dannon

On Wed, May 16, 2018 at 9:48 AM Previti <
christopher.prev...@dkfz-heidelberg.de> wrote:

> Hi,
>
> I just implemented a couple of features (impersonate/delete users) that
> I'm going to use for troubleshooting due to the fact that this might be an
> issue that is specific to us.
>
> I think it might be an issue with the user-accounts themselves...they're
> "artificial" in a sense that they are called "course1" through "course10"
> (as username and password) and all associated with the same email address...
>
> Could this be problematic in general?
> Cheers,
> Christopher
>
> On 05/16/2018 02:35 PM, Dannon Baker wrote:
>
> I definitely have not seen this before, and am not able to reproduce it on
> my local instance.  Can you provide a screenshot of what you're seeing, and
> the organization of the histories that are being sourced for the incorrect
> datasets?
>
> On Wed, May 16, 2018 at 7:25 AM Previti <
> christopher.prev...@dkfz-heidelberg.de> wrote:
>
>> Dear all,
>>
>> I'm having a strange issue with Trackster in our Galaxy implementation.
>>
>> Users seem to be able to upload files ("Add Datasets") from* all *histories
>> of all users, regardless of ownership.
>>
>> ...is this something that has been observed before...? How do I stop this
>> from happening?
>>
>> Thanks and best regards,
>>
>> Christopher
>> --
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4661
>>
>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>> www.dkfz.de
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>> VAT-ID No.: DE143293537
>>
>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
>> Personen bestimmt, an die sie adressiert ist.
>> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
>> Informationen enthalten. Sollten Sie nicht
>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender
>> und löschen Sie die Mitteilung.
>> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
>> untersagt.
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/
>
>
> --
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4661
>
> christopher.prev...@dkfz.de <http://www.dkfz.de/>
> www.dkfz.de
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender
> und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
> untersagt.
>
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Re: [galaxy-dev] Trackster ownership issue

[Dannon Baker]

I definitely have not seen this before, and am not able to reproduce it on
my local instance.  Can you provide a screenshot of what you're seeing, and
the organization of the histories that are being sourced for the incorrect
datasets?

On Wed, May 16, 2018 at 7:25 AM Previti <
christopher.prev...@dkfz-heidelberg.de> wrote:

> Dear all,
>
> I'm having a strange issue with Trackster in our Galaxy implementation.
>
> Users seem to be able to upload files ("Add Datasets") from* all *histories
> of all users, regardless of ownership.
>
> ...is this something that has been observed before...? How do I stop this
> from happening?
>
> Thanks and best regards,
>
> Christopher
> --
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4661
>
> christopher.prev...@dkfz.de 
> www.dkfz.de
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender
> und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
> untersagt.
>
>
>  ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
___
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Re: [galaxy-dev] V18.01 'View all histories' doesn't work

[Dannon Baker]

Yep, I've reproduced the problem here and will work on a fix.  Here's a
github issue if you'd like to follow progress:
https://github.com/galaxyproject/galaxy/issues/6145

On Tue, May 15, 2018 at 12:42 PM Ping Luo  wrote:

> Yes, we are hosting it at a prefix.
>
> On Tue, May 15, 2018 at 11:30 AM, Dannon Baker 
> wrote:
>
>> Are you perhaps hosting at a prefix using proxy-prefix (so, instead of
>> `/api/histories` we should be looking for `/mygalaxy/api/histories`, or the
>> like)?  I'll take a quick look, this should be an easy fix.
>>
>> On Tue, May 15, 2018 at 12:25 PM Ping Luo  wrote:
>>
>>> The Galaxy log file shows:
>>>  [15/May/2018:11:20:44 -0500] "GET /template/api/webhooks HTTP/1.1" 200
>>> - "https://xxx.xxx.xxx/template/history/view_multiple"; "Mozilla/5.0
>>> (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
>>> Chrome/66.0.3359.170 Safari/537.36"
>>>
>>> The apache log file shows:
>>>  [15/May/2018:11:20:44 -0500] "GET
>>> /api/histories?limit=1&offset=0&order=update_time&view=dev-detailed&q=encoded_id-in&q=deleted&qv=2e2f04bac8f3fcbc&qv=None
>>> HTTP/1.1" 404 211
>>>
>>> Where else can I find more information?
>>>
>>>
>>> On Tue, May 15, 2018 at 11:03 AM, Devon Ryan  wrote:
>>>
>>>> You’ll probably get a more informative error message if you check the
>>>> logs.
>>>>
>>>> Sent from my iPhone
>>>>
>>>> > On 15. May 2018, at 17:45, Ping Luo  wrote:
>>>> >
>>>> > I just installed Galaxy V18.01. I got an error when clicking 'View
>>>> all histories' in the history tool bar 
>>>> >
>>>> > The error says 'The requested URL /api/histories was not found on
>>>> this server'.
>>>> > 
>>>> >
>>>> > Is there anyone experiencing the same problem?
>>>> >
>>>> > Ping
>>>> > ___
>>>> > Please keep all replies on the list by using "reply all"
>>>> > in your mail client.  To manage your subscriptions to this
>>>> > and other Galaxy lists, please use the interface at:
>>>> >  https://lists.galaxyproject.org/
>>>> >
>>>> > To search Galaxy mailing lists use the unified search at:
>>>> >  http://galaxyproject.org/search/
>>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/
>>
>>
>
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Re: [galaxy-dev] V18.01 'View all histories' doesn't work

[Dannon Baker]

Are you perhaps hosting at a prefix using proxy-prefix (so, instead of
`/api/histories` we should be looking for `/mygalaxy/api/histories`, or the
like)?  I'll take a quick look, this should be an easy fix.

On Tue, May 15, 2018 at 12:25 PM Ping Luo  wrote:

> The Galaxy log file shows:
>  [15/May/2018:11:20:44 -0500] "GET /template/api/webhooks HTTP/1.1" 200 - "
> https://xxx.xxx.xxx/template/history/view_multiple"; "Mozilla/5.0 (Windows
> NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/66.0.3359.170 Safari/537.36"
>
> The apache log file shows:
>  [15/May/2018:11:20:44 -0500] "GET
> /api/histories?limit=1&offset=0&order=update_time&view=dev-detailed&q=encoded_id-in&q=deleted&qv=2e2f04bac8f3fcbc&qv=None
> HTTP/1.1" 404 211
>
> Where else can I find more information?
>
>
> On Tue, May 15, 2018 at 11:03 AM, Devon Ryan  wrote:
>
>> You’ll probably get a more informative error message if you check the
>> logs.
>>
>> Sent from my iPhone
>>
>> > On 15. May 2018, at 17:45, Ping Luo  wrote:
>> >
>> > I just installed Galaxy V18.01. I got an error when clicking 'View all
>> histories' in the history tool bar 
>> >
>> > The error says 'The requested URL /api/histories was not found on this
>> server'.
>> > 
>> >
>> > Is there anyone experiencing the same problem?
>> >
>> > Ping
>> > ___
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >  https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >  http://galaxyproject.org/search/
>>
>
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Re: [galaxy-dev] User Registration Error

[Dannon Baker]

Do you think you may have run Galaxy previously as root (using sudo?).
This could potentially create these compiled template files under a
different user, preventing a non-root user from overwriting them.

In any event, it's safe to `rm -r database/compiled_templates`, and allow
them to be regenerated.

On Tue, Jan 16, 2018 at 4:00 PM, Thomas, Dallas 
wrote:

> Help Please,
>
>
>
> So I am feeling a bit dumb right now.  I have set-up another local Galaxy
> test server and have enabled all of the user authentication stuff in the
> galaxy.ini.  I am using nginx for proxy however am not using the external
> authentication or remote.  Every time a user clicks on the User->Register –
> there is the following error:
>
>
> Internal Server Error Galaxy was unable to successfully complete your
> request
>
> URL: http://10.115.0.65:8080/user/create
> Module galaxy.web.framework.middleware.error:*149* in __call__
> >>  app_iter *=* self*.*application
> *(*environ*,* sr_checker*)*
> Module paste.recursive:*84* in __call__
> >>  *return* self*.*application*(*
> environ*,* start_response*)*
> Module paste.httpexceptions:*633* in __call__
> >>  *return* self*.*application*(*
> environ*,* start_response*)*
> Module galaxy.web.framework.base:*133* in __call__
> >>  *return* self*.*handle_request*(*
> environ*,* start_response *)*
> Module galaxy.web.framework.base:*191* in handle_request
> >>  body *=* method*(* trans*,* 
> kwargs *)*
> Module galaxy.webapps.galaxy.controllers.user:*746* in create
> >>  status*=*status *)*
> Module galaxy.web.framework.webapp:*810* in fill_template
> >>  *return* self*.*
> fill_template_mako*(* filename*,* kwargs *)*
> Module galaxy.web.framework.webapp:*818* in fill_template_mako
> >>  template *=* template_lookup*.*
> get_template*(* filename *)*
> Module mako.lookup:*218* in get_template
> >>  *return* self*.*_load*(*srcfile
> *,* uri*)*
> Module mako.lookup:*283* in _load
> >>  self*.*template_args*)*
> Module mako.template:*218* in __init__
> >>  module *=* self*.*
> _compile_from_file*(*path*,* filename*)*
> Module mako.template:*245* in _compile_from_file
> >>  module *=* imp*.*load_source*(*
> self*.*module_id*,* path*,* open*(*path*,* 'rb'*))*
> *IOError: [Errno 13] Permission denied:
> '/home/galaxy/galaxy_dist/database/compiled_templates/user/register.mako.py
> '*
> extra data 
>
>
> full traceback 
>
> text version 
>
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
>
>
>
> Any help would be very much appreciated.
>
>
>
> Sincerely
>
> Dallas Thomas
>
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Re: [galaxy-dev] html with styles

[Dannon Baker]

No, it's a good question!

The primarily concern is malicious javascript which could be used to
compromise a user's account or otherwise act on their behalf.  Javascript
is of course stripped out by the sanitizer, but it's also possible to embed
javascript in CSS files (I think at this point only in older browsers), so
to be safe we disable all that unless a tool is explicitly marked trusted.

-Dannon

On Fri, Nov 3, 2017 at 12:58 PM, Wolfgang Maier <
wolfgang.ma...@biologie.uni-freiburg.de> wrote:

> Maybe a dumb follow-up question, but I just don't know much about web
> server security:
>
> Why does sanitization have to care about in-document style information?
>
>
> On 03.11.2017 17:49, Dannon Baker wrote:
>
>> Hi Wolfgang,
>>
>> As a security measure, we added sanitization by default of content
>> displayed as HTML.  Local galaxy administrators can use the display
>> whitelist (left side of the admin window) to configure 'safe' applications,
>> which will then no longer be sanitized on display.  Let me know if this
>> doesn't solve the problem for you!
>>
>> -Dannon
>>
>> On Fri, Nov 3, 2017 at 12:37 PM, Wolfgang Maier <
>> wolfgang.ma...@biologie.uni-freiburg.de <mailto:wolfgang.maier@biologi
>> e.uni-freiburg.de>> wrote:
>>
>> Dear all,
>>
>> until recently extra html files linked from html datasets got
>> displayed with style information applied, but this seems to have
>> changed.
>> I did not investigate the change in detail, but is this a
>> consequence of the backported
>> https://docs.galaxyproject.org/en/master/releases/17.09_anno
>> unce.html#cross-site-scripting-and-session-fixation
>> <https://docs.galaxyproject.org/en/master/releases/17.09_ann
>> ounce.html#cross-site-scripting-and-session-fixation>?
>>
>> Is downloading the zipped data and opening it locally now the only
>> way to view styled html?
>>
>> Have a nice weekend,
>> Wolfgang
>> ___
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>>
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>>
>>
>>
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Re: [galaxy-dev] html with styles

[Dannon Baker]

Hi Wolfgang,

As a security measure, we added sanitization by default of content
displayed as HTML.  Local galaxy administrators can use the display
whitelist (left side of the admin window) to configure 'safe' applications,
which will then no longer be sanitized on display.  Let me know if this
doesn't solve the problem for you!

-Dannon

On Fri, Nov 3, 2017 at 12:37 PM, Wolfgang Maier <
wolfgang.ma...@biologie.uni-freiburg.de> wrote:

> Dear all,
>
> until recently extra html files linked from html datasets got displayed
> with style information applied, but this seems to have changed.
> I did not investigate the change in detail, but is this a consequence of
> the backported https://docs.galaxyproject.org
> /en/master/releases/17.09_announce.html#cross-site-scripting
> -and-session-fixation?
>
> Is downloading the zipped data and opening it locally now the only way to
> view styled html?
>
> Have a nice weekend,
> Wolfgang
> ___
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Re: [galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

[Dannon Baker]

Thanks for the enhancement idea, I've made an issue for it here:
https://github.com/galaxyproject/galaxy/issues/4162

On Wed, Jun 7, 2017 at 5:50 AM SAPET, Frederic 
wrote:

> hello
>
>
>
> just like Floreline :
>
>
> http://dev.list.galaxyproject.org/Paste-Fetch-data-indicate-filename-before-download-data-default-Pasted-Entry-td4670124.html
>
> some of my colleagues ask me if it could be possible to rename the
> uploaded ( from pasted data)  file before the download.
>
> I would like to know if it could be added as an enhancement for a future
> release ?
>
>
>
> thank you
>
>
>
> Fred
>
>
>
> ---
>
> Frederic Sapet
>
> Bioinformatics Research Engineer
>
> BIOGEMMA - Upstream Genomics Group
>
> Centre de Recherche de Chappes
>
> CS 90126
>
> 63720 CHAPPES
>
> FRANCE
>
> Tel : +33 (0)4 73 67 88 54 <+33%204%2073%2067%2088%2054>
>
> Fax : +33 (0)4 73 67 88 99 <+33%204%2073%2067%2088%2099>
>
> E-mail : frederic.sa...@biogemma.com
>
>
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Re: [galaxy-dev] Dataset Cleanup

[Dannon Baker]

The quota usage can occasionally get out of sync with reality.  If you're
an admin user, go to /admin/users, select a user, and you should
be able to recalculate the quota to verify it is correct.  There's also a
script distributed with Galaxy (/scripts/set_user_disk_usage.py) that
allows you to recalculate across all users.  Let me know if this wasn't
your issue and I can think of other possible causes.

-Dannon

On Thu, Jan 5, 2017 at 5:17 PM, McCully, Dwayne (NIH/NIAMS) [C] <
dmccu...@mail.nih.gov> wrote:

> Strange since I've deleted almost everything from my Galaxy account and it
> still says 59 GB and
> another user is having the same problem.   Is there a way to tie the
> dataset or history to the user?
> I can then ask them to delete them.
>
> Dwayne
>
> -Original Message-
> From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
> Sent: Thursday, January 05, 2017 9:43 AM
> To: McCully, Dwayne (NIH/NIAMS) [C] ;
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Dataset Cleanup
>
> Hi,
>
> this script only deletes files that are marked as deleted. So it might be
> that users have old histories and this data will not be removed.
>
> For you account and the used-space. Please go to your admin section, to
> users, your user-name and there should be an option to recalculate the
> disc-usage for your user.
>
> Hope this helps,
> Bjoern
>
> Am 03.01.2017 um 16:41 schrieb McCully, Dwayne (NIH/NIAMS) [C]:
> > Hello Everyone,
> >
> >
> >
> > I have datasets that go back over a year in the files/000 directory
> > but running the following script does not delete the datasets.
> >
> > Also, my account says I have 59 GB used and can’t figure out where
> > it’s getting that number.  I have almost everything deleted
> >
> > in my Galaxy account.
> >
> >
> >
> > galaxy_clean.sh
> >
> > #!/bin/sh -x
> >
> >
> >
> > /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_hist
> > ories.sh
> >
> > /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh
> >
> > /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh
> >
> > /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh
> >
> > /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh
> >
> > /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh
> >
> > Exit
> >
> >
> >
> >
> >
> > Any information on this issue would be appreciated.
> >
> >
> >
> > Dwayne
> >
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this and other
> > Galaxy lists, please use the interface at:
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> >
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> >
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Re: [galaxy-dev] More problems installing Galaxy

[Dannon Baker]

Hernan,

Sorry for the slow response here, have you made any progress?  I'd be glad
to help sort this out.

Instead of creating an alias to a particular python in your .bashrc, I'd
recommend that if you're having problems you should manually create the
virtualenv with the specific python version you want.  Once you've done
that, on galaxy's first start, it'll populate the requirements correctly.

An example command would be:

virtualenv -p /usr/local/bin/python2.7 .venv

Execute this command from the galaxy directory, and it'll create a
virtualenv named .venv, which is what Galaxy expects to use.  After that,
just start Galaxy and the requirements should be installed to .venv
automatically.

-Dannon

On Wed, Nov 9, 2016 at 2:39 PM, Hernán Piqueras  wrote:

> I have a Linux with both Python 2.6 and Python 2.7. Apparently Python is
> so bad designed that you cannot simply upgrade from 2.6 to 2.7 without
> breaking your system. As latest Galaxy works with Python 2.7, I put an
> alias in my .bashrc to /usr/local/bin/python2.7 and the same with
> virtualenv. I also enabled bash debugging and enabled expanded alias into
> .sh scripts.
>
>
> Then I ran :
>
>
> $ sh galaxy/run.sh
>
>
> ... lots of output ---
>
> Requirement already satisfied: pysam==0.8.4+gx1 in
> ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70))
> Requirement already satisfied: PasteScript in 
> ./.venv/lib/python2.7/site-packages
> (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 51))
> ++ PYTHONPATH=lib
> ++ /usr/local/bin/python2.7 -c 'import galaxy.dependencies; print
> '\''\n'\''.join(galaxy.dependencies.optional('\''config/galaxy.ini'\''))'
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9,
> in 
> from galaxy.util import asbool
>   File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in
> 
> from six import binary_type, iteritems, PY3, string_types, text_type
> ImportError: No module named six
> + GALAXY_CONDITIONAL_DEPENDENCIES=
> + exit 1
>
>
> If I check with root user, six package is installed. My guess was I
> am missing an alias to pip2.7, then I added such alias in my .bashrc and
> again:
>
>
> $ sh galaxy/run.sh
>
>
> ... lots of output ---
>
> ++ '[' -n /bin/bash -o -n '' ']'
> ++ hash -r
> + unset PYTHONPATH
> + '[' -z /home/galaxy/galaxy/.venv ']'
> + : https://wheels.galaxyproject.org/simple
> + '[' 1 -eq 1 ']'
> + /usr/local/bin/pip2.7 install 'pip>=8.1'
> Traceback (most recent call last):
>   File "/usr/local/bin/pip2.7", line 5, in 
> from pkg_resources import load_entry_point
>   File "/usr/local/lib/python2.7/site-packages/distribute-0.6.
> 44-py2.7.egg/pkg_resources.py", line 2850, in 
> working_set.require(__requires__)
>   File "/usr/local/lib/python2.7/site-packages/distribute-0.6.
> 44-py2.7.egg/pkg_resources.py", line 696, in require
> needed = self.resolve(parse_requirements(requirements))
>   File "/usr/local/lib/python2.7/site-packages/distribute-0.6.
> 44-py2.7.egg/pkg_resources.py", line 594, in resolve
> raise DistributionNotFound(req)
> pkg_resources.DistributionNotFound: pip==9.0.1
>
> # pip --version
> pip 9.0.1 from /usr/local/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg
> (python 2.7)
> I have installed Python 2.7 and its tools (virtualenv, pip, etc) following
> official guidelines.
>
>
> How can install the missing dependecies?
>
>
>
>
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Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used

[Dannon Baker]

Unfortunately we weren't able to use pandoc, coming from Moin.

Regarding edit links, yes, that's exactly what we have implemented.

-Dannon

On Tue, Nov 15, 2016 at 10:26 AM, Peter Cock 
wrote:

> Thanks Dannon,
>
> I've logged the universe_wsgi.ini issue there as
> https://github.com/galaxyproject/galaxy-site/issues/16
>
> Interesting to see yet another MediaWiki site being moved to
> GitHub with Markdown - although not with GitHub pages in this
> case. I'd guess you guys used the wonderful pandoc for the
> conversion?
>
> I assume you'll be able to add "edit" buttons to pages pointing
> at the markdown pages on GitHub? While it could be prettier,
> this works pretty well for us using GitHub Pages:
>
> https://github.com/biopython/biopython.github.io/pull/78
>
> Regards,
>
> Peter
>
> On Tue, Nov 15, 2016 at 3:10 PM, Dannon Baker 
> wrote:
> > Hi Peter,
> >
> > We're in the middle of migrating the wiki right now -- you may notice
> that
> > the current wiki is in read-only mode.  Going forward, the place to
> report
> > (and fix) issues like that will be
> > https://github.com/galaxyproject/galaxy-site.
> >
> > -Dannon
> >
> > On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock 
> > wrote:
> >>
> >> Hello all,
> >>
> >> Is there a specific issue tracker for the wiki? It seems wrong to
> >> open an issue on the main GitHub code repository...
> >>
> >> e.g. Many of the documentation pages still refer to the legacy
> >> configuration filename universe_wgsi.ini rather than the new
> >> name of config/galaxy.ini
> >>
> >> Problem pages include:
> >>
> >> https://wiki.galaxyproject.org/Learn/SecurityFeatures
> >> https://wiki.galaxyproject.org/Admin/DiskQuotas
> >> https://wiki.galaxyproject.org/Admin/SampleTracking/Demo
> >> https://wiki.galaxyproject.org/Admin/Tools/MultipleOutputFiles
> >> https://wiki.galaxyproject.org/Admin/Config/GenomeSpace
> >> https://wiki.galaxyproject.org/Admin/Config/ApacheExternalUserAuth
> >> https://wiki.galaxyproject.org/VisualizationSetup
> >> https://wiki.galaxyproject.org/ToolShedApi
> >>
> >> Other pages would benefit from minor edits to at least put the old form
> >> second and in brackets:
> >>
> >> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
> >> https://wiki.galaxyproject.org/Admin/Interface
> >> https://wiki.galaxyproject.org/ToolShed/InstallingRepositoriesToGalaxy
> >> Some pages look fine, e.g.
> >>
> >> https://wiki.galaxyproject.org/ToolShed/InstallingAndCompilingPackages
> >>
> >> Or are clearly dated and appropriate for the time, e.g. Dev news briefs
> >>
> >> https://wiki.galaxyproject.org/DevNewsBriefs/2010_07_16
> >>
> >> This means lots of pages with the term which are fine:
> >>
> >>
> >> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=
> fullsearch&titlesearch=0&from=0&value=universe_wsgi.ini
> >>
> >> Regards,
> >>
> >> Peter
> >> ___
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>   https://lists.galaxyproject.org/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>   http://galaxyproject.org/search/mailinglists/
> >
> >
>
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Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used

[Dannon Baker]

Hi Peter,

We're in the middle of migrating the wiki right now -- you may notice that
the current wiki is in read-only mode.  Going forward, the place to report
(and fix) issues like that will be
https://github.com/galaxyproject/galaxy-site.

-Dannon

On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock 
wrote:

> Hello all,
>
> Is there a specific issue tracker for the wiki? It seems wrong to
> open an issue on the main GitHub code repository...
>
> e.g. Many of the documentation pages still refer to the legacy
> configuration filename universe_wgsi.ini rather than the new
> name of config/galaxy.ini
>
> Problem pages include:
>
> https://wiki.galaxyproject.org/Learn/SecurityFeatures
> https://wiki.galaxyproject.org/Admin/DiskQuotas
> https://wiki.galaxyproject.org/Admin/SampleTracking/Demo
> https://wiki.galaxyproject.org/Admin/Tools/MultipleOutputFiles
> https://wiki.galaxyproject.org/Admin/Config/GenomeSpace
> https://wiki.galaxyproject.org/Admin/Config/ApacheExternalUserAuth
> https://wiki.galaxyproject.org/VisualizationSetup
> https://wiki.galaxyproject.org/ToolShedApi
>
> Other pages would benefit from minor edits to at least put the old form
> second and in brackets:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
> https://wiki.galaxyproject.org/Admin/Interface
> https://wiki.galaxyproject.org/ToolShed/InstallingRepositoriesToGalaxy
> Some pages look fine, e.g.
>
> https://wiki.galaxyproject.org/ToolShed/InstallingAndCompilingPackages
>
> Or are clearly dated and appropriate for the time, e.g. Dev news briefs
>
> https://wiki.galaxyproject.org/DevNewsBriefs/2010_07_16
>
> This means lots of pages with the term which are fine:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=
> fullsearch&titlesearch=0&from=0&value=universe_wsgi.ini
>
> Regards,
>
> Peter
> ___
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Re: [galaxy-dev] purge dataset at a different location

[Dannon Baker]

Hi Mark,

I'm not sure this is something I'd encourage pursuing for most folks, but I
understand that custom deployments may need special functionality.  To
implement this for your Galaxy instance, you'd want to look at the
ObjectStore "delete" functions, here:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/objectstore/__init__.py#L375

-Dannon

On Thu, Nov 3, 2016 at 12:33 AM, Mark Xiao  wrote:

> Dear Galaxy Developers,
>
> Because of specific use case, our transfer tool need to keep the datasets
> in a different location instead of the default location, so we'd like to
> purge datasets according to its "external_filename" (we found this column
> in the dataset table in the database). Is there a way or some code to
> modify so that when we try to purge a dataset or a history in Galaxy, the
> file located at a dataset's external_filename can also be deleted?
>
> Thanks in advance,
> Mark Xiao
>
> ___
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> in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Question about Galaxy integration with external access control

[Dannon Baker]

Hi Simon,

On Thu, Sep 29, 2016 at 11:22 AM, Simon Chang 
wrote:
>
> 1)  Assuming Galaxy can read LDAP directory service information, to what
> extent is access control enforced?  Is it on a file system level?
>

The 'galaxy' user, or whichever user is running the files is the normal way
to handle this, with other system users not being able to access galaxy
owned files directly.

2)  If a researcher logs into Galaxy with his LDAP credentials, runs some
> analyses and obtains the results, how exactly are these results protected
> from other researchers who may be prohibited from accessing these results
> due to institutional policies?  Accordingly, if a researcher wants to share
> the data product with another LDAP user, how is that done exactly apart
> from simply downloading and emailing it?
>

Check out https://wiki.galaxyproject.org/Learn/Share for more information
about galaxy's sharing abilities, and certainly feel free to ask more
questions.  In short, there are systems built into Galaxy that allow users
to share (or secure) Galaxy objects within the framework.

-Dannon
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Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

[Dannon Baker]

Ok, so it should be gone, I guess.  Check 'git status', maybe it's just
there as an untracked file (and if so, just rm it)?

On Fri, Aug 26, 2016 at 12:55 PM, D K  wrote:

> Hi Dannon,
>
> There's your commit where you describe removing it. So why is it still
> there if I did a git pull (did I do this incorrectly?)?
>
> I did a "git log -- cloudlaunch.py" and got the following:
>
> commit 303597e48a8503aac09c33910aa5482a374f06a1
> Author: Dannon Baker 
> Date:   Wed Aug 12 14:17:44 2015 -0400
>
> Remove old cloudlaunch in favor of https://github.com/
> galaxyproject/cloudlaunch, at launch.usegalaxy.org
>
> commit 6049a7446897baea74c33a5286b6c086c9da31a8
> Author: Dannon Baker 
> Date:   Tue Jul 21 14:03:22 2015 -0400
>
> Catch and return error message during key verification in cloudlaunch.
>
> commit 09719b884806fe1da24b2f7be0f159f1d3b06d04
> Author: dannon 
> Date:   Sat Mar 7 22:51:35 2015 -0500
>
> Cleanup in pbed_to_lped converter
> .
> .
> .
>
>
> On Fri, Aug 26, 2016 at 9:49 AM, Dannon Baker 
> wrote:
>
>> Can you check the git log for that controller, to see how it got added
>> back to, or remained in, the codebase?
>>
>> On Fri, Aug 26, 2016, 12:40 PM D K  wrote:
>>
>>> Hi Dannon,
>>>
>>> Yes, the 
>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py"
>>> does still exist.
>>>
>>> If it's relevant I did a:
>>>
>>> git commit -a -m 'changes made locally prior to upgrade to 16.07'
>>> git pull origin master
>>>
>>> I had to move the file "lib/galaxy/datatypes/checkers.py" but otherwise
>>> didn't get any other errors
>>>
>>>
>>> On Fri, Aug 26, 2016 at 9:38 AM, Dannon Baker 
>>> wrote:
>>>
>>>> Can you check to see if that file (/remote/home/galaxyd/tmp/gala
>>>> xy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py) does still
>>>> exist?  If it does not, it may be a leftover .pyc file (which you can
>>>> delete safely).  If you'd like to just clean out *all* the compiled python
>>>> (which is also safe), run something like ```find  -name "*.pyc"
>>>> -delete```.
>>>>
>>>> On Fri, Aug 26, 2016 at 12:35 PM, D K  wrote:
>>>>
>>>>> I have modified some files in my own local galaxy commit (I think only
>>>>> the sniffers in lib/galaxy/datatypes)
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Aug 26, 2016 at 9:31 AM, Dannon Baker 
>>>>> wrote:
>>>>>
>>>>>> Hey DK,
>>>>>>
>>>>>> The cloudlaunch controller was deprecated and should not be in
>>>>>> 16.07.  Is this a custom modification you have?
>>>>>>
>>>>>> -Dannon
>>>>>>
>>>>>> On Fri, Aug 26, 2016 at 12:30 PM, D K 
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Galaxy-devs,
>>>>>>>
>>>>>>> I just tried upgrading to 16.07 from 16.01 and get this error when
>>>>>>> starting up:
>>>>>>>
>>>>>>>
>>>>>>>> Traceback (most recent call last):
>>>>>>>>   File "./scripts/paster.py", line 26, in 
>>>>>>>> serve.run()
>>>>>>>>   File 
>>>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>>>> line 1061, in run
>>>>>>>> invoke(command, command_name, options, args[1:])
>>>>>>>>   File 
>>>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>>>> line 1067, in invoke
>>>>>>>> exit_code = runner.run(args)
>>>>>>>>   File 
>>>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>>>> line 223, in run
>>>>>>>> result = self.command()
>>>>>>>>   File 
>>>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>>>> line 639, in command
>>>>>>>> app = loadapp( app_spec, name=app_name, relative_to=base,
>>>

Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

[Dannon Baker]

Can you check the git log for that controller, to see how it got added back
to, or remained in, the codebase?

On Fri, Aug 26, 2016, 12:40 PM D K  wrote:

> Hi Dannon,
>
> Yes, the
> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py"
> does still exist.
>
> If it's relevant I did a:
>
> git commit -a -m 'changes made locally prior to upgrade to 16.07'
> git pull origin master
>
> I had to move the file "lib/galaxy/datatypes/checkers.py" but otherwise
> didn't get any other errors
>
>
> On Fri, Aug 26, 2016 at 9:38 AM, Dannon Baker 
> wrote:
>
>> Can you check to see if that file (/remote/home/galaxyd/tmp/
>> galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py) does still
>> exist?  If it does not, it may be a leftover .pyc file (which you can
>> delete safely).  If you'd like to just clean out *all* the compiled python
>> (which is also safe), run something like ```find  -name "*.pyc"
>> -delete```.
>>
>> On Fri, Aug 26, 2016 at 12:35 PM, D K  wrote:
>>
>>> I have modified some files in my own local galaxy commit (I think only
>>> the sniffers in lib/galaxy/datatypes)
>>>
>>>
>>>
>>> On Fri, Aug 26, 2016 at 9:31 AM, Dannon Baker 
>>> wrote:
>>>
>>>> Hey DK,
>>>>
>>>> The cloudlaunch controller was deprecated and should not be in 16.07.
>>>> Is this a custom modification you have?
>>>>
>>>> -Dannon
>>>>
>>>> On Fri, Aug 26, 2016 at 12:30 PM, D K  wrote:
>>>>
>>>>> Hi Galaxy-devs,
>>>>>
>>>>> I just tried upgrading to 16.07 from 16.01 and get this error when
>>>>> starting up:
>>>>>
>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>   File "./scripts/paster.py", line 26, in 
>>>>>> serve.run()
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>> line 1061, in run
>>>>>> invoke(command, command_name, options, args[1:])
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>> line 1067, in invoke
>>>>>> exit_code = runner.run(args)
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>> line 223, in run
>>>>>> result = self.command()
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>>>> line 639, in command
>>>>>> app = loadapp( app_spec, name=app_name, relative_to=base,
>>>>>> global_conf=vars)
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 292, in loadapp
>>>>>> return loadobj(APP, uri, name=name, **kw)
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 317, in loadobj
>>>>>> return context.create()
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 755, in create
>>>>>> return self.object_type.invoke(self)
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 274, in invoke
>>>>>> filtered = context.next_context.create()
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 755, in create
>>>>>> return self.object_type.invoke(self)
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 191, in invoke
>>>>>> return fix_call(context.object, context.global_conf,
>>>>>> **context.local_conf)
>>>>>>   File
>>>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>>>> line 94, in fix_c

Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

[Dannon Baker]

Can you check to see if that file (/remote/home/galaxyd/tmp/
galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py) does still
exist?  If it does not, it may be a leftover .pyc file (which you can
delete safely).  If you'd like to just clean out *all* the compiled python
(which is also safe), run something like ```find  -name "*.pyc"
-delete```.

On Fri, Aug 26, 2016 at 12:35 PM, D K  wrote:

> I have modified some files in my own local galaxy commit (I think only the
> sniffers in lib/galaxy/datatypes)
>
>
>
> On Fri, Aug 26, 2016 at 9:31 AM, Dannon Baker 
> wrote:
>
>> Hey DK,
>>
>> The cloudlaunch controller was deprecated and should not be in 16.07.  Is
>> this a custom modification you have?
>>
>> -Dannon
>>
>> On Fri, Aug 26, 2016 at 12:30 PM, D K  wrote:
>>
>>> Hi Galaxy-devs,
>>>
>>> I just tried upgrading to 16.07 from 16.01 and get this error when
>>> starting up:
>>>
>>>
>>>> Traceback (most recent call last):
>>>>   File "./scripts/paster.py", line 26, in 
>>>> serve.run()
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>> line 1061, in run
>>>> invoke(command, command_name, options, args[1:])
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>> line 1067, in invoke
>>>> exit_code = runner.run(args)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>> line 223, in run
>>>> result = self.command()
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>>>> line 639, in command
>>>> app = loadapp( app_spec, name=app_name, relative_to=base,
>>>> global_conf=vars)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 292, in loadapp
>>>> return loadobj(APP, uri, name=name, **kw)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 317, in loadobj
>>>> return context.create()
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 755, in create
>>>> return self.object_type.invoke(self)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 274, in invoke
>>>> filtered = context.next_context.create()
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 755, in create
>>>> return self.object_type.invoke(self)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 191, in invoke
>>>> return fix_call(context.object, context.global_conf,
>>>> **context.local_conf)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 94, in fix_call
>>>> val = callable(*args, **kw)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py",
>>>> line 39, in app_factory
>>>> return paste_app_factory( global_conf, **kwargs )
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py",
>>>> line 76, in paste_app_factory
>>>> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers',
>>>> app )
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/web/framework/webapp.py",
>>>> line 115, in add_ui_controllers
>>>> module = import_module( module_name )
>>>>   File "/opt/rh/python27/root/usr/lib64/python2.7/importlib/__init__.py",
>>>> line 37, in import_module
>>>> __import__(name)
>>>>   File 
>>>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
>>>> line 16, in 
>>>> from galaxy.util.json import dumps
>>>> ImportError: cannot import name dumps
>>>
>>>
>>> Any suggestions?
>>>
>>> Thanks!
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

[Dannon Baker]

Hey DK,

The cloudlaunch controller was deprecated and should not be in 16.07.  Is
this a custom modification you have?

-Dannon

On Fri, Aug 26, 2016 at 12:30 PM, D K  wrote:

> Hi Galaxy-devs,
>
> I just tried upgrading to 16.07 from 16.01 and get this error when
> starting up:
>
>
>> Traceback (most recent call last):
>>   File "./scripts/paster.py", line 26, in 
>> serve.run()
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>> line 1061, in run
>> invoke(command, command_name, options, args[1:])
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>> line 1067, in invoke
>> exit_code = runner.run(args)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>> line 223, in run
>> result = self.command()
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py",
>> line 639, in command
>> app = loadapp( app_spec, name=app_name, relative_to=base,
>> global_conf=vars)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 292, in loadapp
>> return loadobj(APP, uri, name=name, **kw)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 317, in loadobj
>> return context.create()
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 755, in create
>> return self.object_type.invoke(self)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 274, in invoke
>> filtered = context.next_context.create()
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 755, in create
>> return self.object_type.invoke(self)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 191, in invoke
>> return fix_call(context.object, context.global_conf,
>> **context.local_conf)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 94, in fix_call
>> val = callable(*args, **kw)
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py",
>> line 39, in app_factory
>> return paste_app_factory( global_conf, **kwargs )
>>   File 
>> "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py",
>> line 76, in paste_app_factory
>> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
>>   File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/web/framework/webapp.py",
>> line 115, in add_ui_controllers
>> module = import_module( module_name )
>>   File "/opt/rh/python27/root/usr/lib64/python2.7/importlib/__init__.py",
>> line 37, in import_module
>> __import__(name)
>>   File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/
>> galaxy/controllers/cloudlaunch.py", line 16, in 
>> from galaxy.util.json import dumps
>> ImportError: cannot import name dumps
>
>
> Any suggestions?
>
> Thanks!
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Galaxy Workflow delete intermediate files

[Dannon Baker]

Hi DK,

This isn't currently possible, but you're not the first person to request
this feature -- it should be straightforward to implement and I'll try to
bump it up my priority list a bit.

-Dannon

On Tue, Aug 16, 2016 at 6:25 PM, D K  wrote:

> Hi Galaxy-devs
>
> I've created a workflow that processes some NGS data. Since many of the
> intermediate files are really large, is it possible to automatically delete
> (rather than just hide) some of these files? I've seen that you can delete
> intermediate files that aren't used as inputs to other tools but didn't see
> a way from within the interface to delete other files created by the
> workflow that are used as inputs to other tools (but are not needed after
> the workflow has completed).
>
> Thanks!
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>
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Re: [galaxy-dev] Adding a download link to the "Download or Export Workflow" page with load balancing

[Dannon Baker]

Hey, no problem Alex.  I wonder if you might be running into a uwsgi bug I
fixed a little while back.  Can you test your modifications to galaxy using
a version that includes https://github.com/galaxyproject/galaxy/pull/2630?



On Aug 9, 2016 5:02 PM, "Alex Rodriguez"  wrote:

> Hi Dannon,
> Sorry for the delay in getting back to you. Below are the configuration
> changes we do to get load balancing set.
> We are installing the following packages on the machine:
>
> Install packages:
> apt-get install build-essential
> apt-get install python-dev
> pip install uwsgi
>
> =
>
> In the galaxy.ini file we are making the following modifications:
>
> config galaxy.ini:
> [uwsgi]
> processes = 8
> stats = 127.0.0.1:9191
> socket = 127.0.0.1:8080
> pythonpath = lib
> threads = 4
> logto = /var/log/genomics/galaxy.log
> master = True
>
> [app:main]
> static_enabled = False
> track_jobs_in_database = True
>
> =
>
> And for Nginx we make the following modifications:
>
> In Nginx config, add:
> uwsgi_read_timeout 180;
>
> location / {
> uwsgi_pass 127.0.0.1:8080;
> uwsgi_param UWSGI_SCHEME $scheme;
> include uwsgi_params;
> }
>
> =
>
> Any suggestions will help greatly!
>
> Thanks,
>
> Alex
>
>
> On Jul 25, 2016, at 8:35 AM, Dannon Baker  wrote:
>
> Can you elaborate on the load balancing that you've implemented which
> seems to be causing the problem?  This might help figure out what's going
> on.
>
> On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez 
> wrote:
>
>> Dear Galaxy developers,
>> I am interested in adding a download link to the “Download or Export
>> Workflow” page of a workflow. I am able to add the link through the files
>> in the templates directory and correctly add the necessary API functions in
>> the lib/webapps/galaxy/controllers/workflow.py file.
>> I wanted to ask for some help in figuring out what I might be missing
>> when I try to download a file when I have load balancing feature activated.
>> The page looks something like this:
>> Download to FileDownload workflow to file so that it can be saved or
>> imported into another Galaxy server.
>> <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-workshop-imported-from-uploaded-file-1/json-download>
>>
>> New Test Download ( test file)
>> URL for Importing to Another GalaxyThis workflow must be accessible
>> before it can be imported into another Galaxy.
>> <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c>
>>
>>
>> As you can see I added the “New test Download” link.
>> I have added and tested the function which gets me the information about
>> the workflow I want correctly. For now it’s just a “hello world” string.
>> When I don’t use load balancing I get the contents I want downloaded to
>> the file correctly.
>> However, when I activate load balancing, it only downloads an empty file.
>> I can print the contents of the test download file to the galaxy log, but
>> as I said nothing gets printed on the actual file.
>>
>> Is there some javascript code I also need to add for this functionality
>> that I might be missing such that the download works with load balancing?
>> As I mentioned I do get a proper download when load balancing is not
>> activated. BTW, all other existing download links work properly with both
>> load balancing and no load balancing.
>>
>> Thanks,
>>
>> Alex
>>
>>
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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>
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Re: [galaxy-dev] Command line building

[Dannon Baker]

Check out
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/command_factory.py

Let me know if this wasn't what you were looking for.

-Dannon

On Fri, Aug 5, 2016 at 10:49 AM Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Within the galaxy app itself, does anyone know where the command line is
> being built?
> Thanks!
> Katherine
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Re: [galaxy-dev] Retrieving bam index file for visualization outside of Galaxy

[Dannon Baker]

Hi Scott,

This isn't currently exposed through the API, but I'm working on
implementing it at https://github.com/galaxyproject/galaxy/pull/2741, if
you'd like to test it.

-Dannon

On Thu, Aug 4, 2016 at 10:38 AM Ouellette, Scott <
scott_ouelle...@hms.harvard.edu> wrote:

> Hi all,
>
> I have a use case where I need to programmatically download both the
> *.bam* and it's index file to run IGV outside of Galaxy, but have not
> found a straightforward way to do so.
> It seems that Galaxy always generates this *.bai *file under the hood,
> and I can download it manually by clicking the “save” icon on the dataset
> in my history. Although, the application I am coding for relies on the
> bioblend Python library.
>
> ---
>
> In bioblend I see a field returned upon a
> `DatasetClient().show_dataset()` but that is
> as far as I've got:
>
> "meta_files": [
> {
> "file_type": "bam_index"
> }
> ],
>
> Any help is appreciated!
>
> Thanks,
> Scott O.
>
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Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

[Dannon Baker]

The good news is that I found out why this sounds familiar.  The bad news
is that I committed a fix for this way back in 14.08, here:
https://github.com/galaxyproject/galaxy/commit/5769ea88fa90f3f7c22505cd06aa6f83f940a1e,
which is still not working for you (though it does work for my basic
external auth configuration even back on 15.10).

The only thing that comes to mind is that somehow your remote_user_email
isn't matching up with the admin_users list that's generated here.  Are you
using remote_user_maildomain (this actually does not work correctly for me
in 15.10, so I was unable to test that configuration, though I could see
why it might prevent admin_user from matching)?  Any chance you want to add
a debugging statement or two there and look in the logs to see why that URL
isn't being whitelisted for your user?


On Thu, Jul 28, 2016 at 10:50 AM Ryan G  wrote:

> Hi Dannon - We are using 15.10.
>
> We have an Apache Proxy server sitting in front of Galaxy and handling the
> SSO.  There is no non-standard routing in place.   Yes, when I navigate to
> the /user/logout url, I get the "Access to Galaxy user controls is
> disabled" message.
>
>
> On Thu, Jul 28, 2016 at 12:16 AM, Dannon Baker 
> wrote:
>
>> I did a bit of digging here, and it looks to me like /user/logout should
>> be whitelisted in the middleware, and shouldn't present that "Access to
>> Galaxy user controls is disabled".
>>
>> I might need a little more information.  What revision of Galaxy are you
>> running?  Are you serving Galaxy at a subdomain or is any other nonstandard
>> routing in place?  As an admin user, if you just directly navigate
>> to http:///user/logout, you get the same
>> path-blocked error message?
>>
>> On Wed, Jul 27, 2016 at 1:15 PM Ryan G 
>> wrote:
>>
>>> Thanks.  Clearing out the browser history resolved it but there should
>>> be a better way...
>>>
>>> On Wed, Jul 27, 2016 at 12:48 PM, Dannon Baker 
>>> wrote:
>>>
>>>> Hey, thanks for this.  I've made an issue (
>>>> https://github.com/galaxyproject/galaxy/issues/2671)  and will check
>>>> it out today.
>>>>
>>>> On Wed, Jul 27, 2016 at 12:44 PM Ryan G 
>>>> wrote:
>>>>
>>>>> Hi all - We are using a SSO system so that user's authenticate
>>>>> externally from Galaxy.
>>>>>
>>>>> when I impersonate a user then try to log out as that user, I'm unable
>>>>> to.  I get the page "
>>>>> Access to Galaxy user controls is disabled
>>>>>
>>>>> User controls are disabled when Galaxy is configured for external
>>>>> authentication."
>>>>>
>>>>>
>>>>> If I close the browser down, and restart, I get my SSO log in page,
>>>>> but when I get to Galaxy, I'm still impersonating the user.
>>>>>
>>>>>
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>>>>
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Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

[Dannon Baker]

I did a bit of digging here, and it looks to me like /user/logout should be
whitelisted in the middleware, and shouldn't present that "Access to Galaxy
user controls is disabled".

I might need a little more information.  What revision of Galaxy are you
running?  Are you serving Galaxy at a subdomain or is any other nonstandard
routing in place?  As an admin user, if you just directly navigate
to http:///user/logout, you get the same path-blocked
error message?

On Wed, Jul 27, 2016 at 1:15 PM Ryan G  wrote:

> Thanks.  Clearing out the browser history resolved it but there should be
> a better way...
>
> On Wed, Jul 27, 2016 at 12:48 PM, Dannon Baker 
> wrote:
>
>> Hey, thanks for this.  I've made an issue (
>> https://github.com/galaxyproject/galaxy/issues/2671)  and will check it
>> out today.
>>
>> On Wed, Jul 27, 2016 at 12:44 PM Ryan G 
>> wrote:
>>
>>> Hi all - We are using a SSO system so that user's authenticate
>>> externally from Galaxy.
>>>
>>> when I impersonate a user then try to log out as that user, I'm unable
>>> to.  I get the page "
>>> Access to Galaxy user controls is disabled
>>>
>>> User controls are disabled when Galaxy is configured for external
>>> authentication."
>>>
>>>
>>> If I close the browser down, and restart, I get my SSO log in page, but
>>> when I get to Galaxy, I'm still impersonating the user.
>>>
>>>
>>> ___
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>>
>>
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Re: [galaxy-dev] workflow problems

[Dannon Baker]

Yep, thought it was familiar and that we'd fixed it.  Cristel, let us know
if you have trouble with upgrading -- I just confirmed that this isn't an
issue in the current 16.04 release or on the dev branch.

On Wed, Jul 27, 2016 at 10:27 PM Aysam Guerler 
wrote:

> I remember this issue and that it was fixed. Updating to a newer revision
> should resolve it.
>
> On Wed, Jul 27, 2016 at 10:06 PM, Dannon Baker 
> wrote:
>
>> This is indeed weird behavior.  What revision is your Galaxy at?
>>
>> On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas 
>> wrote:
>>
>>> Hi all,
>>> I ran into a weird behavior on my local instance of galaxy and I was
>>> wondering if anyone had the same experience (and if so what did you do to
>>> fix it?).
>>>
>>> When trying to run a workflow by clicking on the workflow name, it
>>> works. When trying to run the workflow by clicking on the arrow next to the
>>> name and then 'run', or by clicking on run from the workflow editor, it
>>> takes me to the interactive tour page.
>>>
>>> Anyone else?
>>>
>>> Thanks,
>>> Cris
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>>
>>
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>
>
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Re: [galaxy-dev] workflow problems

[Dannon Baker]

This is indeed weird behavior.  What revision is your Galaxy at?

On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas 
wrote:

> Hi all,
> I ran into a weird behavior on my local instance of galaxy and I was
> wondering if anyone had the same experience (and if so what did you do to
> fix it?).
>
> When trying to run a workflow by clicking on the workflow name, it works.
> When trying to run the workflow by clicking on the arrow next to the name
> and then 'run', or by clicking on run from the workflow editor, it takes me
> to the interactive tour page.
>
> Anyone else?
>
> Thanks,
> Cris
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Re: [galaxy-dev] Info Page after tool execution

[Dannon Baker]

Hi Katherine,

That'd be this method:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/controllers/dataset.py#L978
Which fills this template:
https://github.com/galaxyproject/galaxy/blob/dev/templates/show_params.mako

On Wed, Jul 27, 2016 at 1:20 PM Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hello Galaxy Community,
> Does anyone know what file would be responsible for creating the info page
> after the execution of a tool? This is the page you access after output has
> been created in the history, by clicking on the little 'i' icon.
> Thanks!
>
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Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

[Dannon Baker]

Hey, thanks for this.  I've made an issue (
https://github.com/galaxyproject/galaxy/issues/2671)  and will check it out
today.

On Wed, Jul 27, 2016 at 12:44 PM Ryan G  wrote:

> Hi all - We are using a SSO system so that user's authenticate externally
> from Galaxy.
>
> when I impersonate a user then try to log out as that user, I'm unable
> to.  I get the page "
> Access to Galaxy user controls is disabled
>
> User controls are disabled when Galaxy is configured for external
> authentication."
>
>
> If I close the browser down, and restart, I get my SSO log in page, but
> when I get to Galaxy, I'm still impersonating the user.
>
>
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Re: [galaxy-dev] DOS attack launched from our Galaxy instance

[Dannon Baker]

Keith,

Did you figure this out?  I'm very curious as to what this was.  Outside
mass admin tool updates, or maybe wheel installation, I can't think of
anything that would have triggered anything like this on the Galaxy side.

-Dannon

On Wed, Jul 13, 2016 at 5:31 PM Suderman Keith 
wrote:

> We are in the process of installing a Galaxy instance to Amazon EC2 and
> this morning I received an email from ec2-ab...@amazon.com saying that
> our EC2 instance has been flooding 45.64.64.40 with data in what looks like
> a DOS attack. A whois shows that the IP belongs to Incapsula, which appears
> to be a load balancing proxy server.  Does anyone here recognize the IP or
> use Incapsula?  My first thought is that something in Galaxy might be
> trying to "phone home".
>
> The Galaxy instance we are using is based on the galaxy-stable:16.04
> Docker image from Björn with a few of our tools installed for testing. I've
> locked down access to the instance until I figure out what happened and I
> wanted to check in here first to see if I’ve been DOS’ing the Galaxy
> infrastructure or if anyone recognizes the IP address.
>
> Keith
>
> --
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
>
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Re: [galaxy-dev] Adding a download link to the "Download or Export Workflow" page with load balancing

[Dannon Baker]

Can you elaborate on the load balancing that you've implemented which seems
to be causing the problem?  This might help figure out what's going on.

On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez 
wrote:

> Dear Galaxy developers,
> I am interested in adding a download link to the “Download or Export
> Workflow” page of a workflow. I am able to add the link through the files
> in the templates directory and correctly add the necessary API functions in
> the lib/webapps/galaxy/controllers/workflow.py file.
> I wanted to ask for some help in figuring out what I might be missing when
> I try to download a file when I have load balancing feature activated. The
> page looks something like this:
> Download to FileDownload workflow to file so that it can be saved or
> imported into another Galaxy server.
> 
>
> New Test Download ( test file)
> URL for Importing to Another GalaxyThis workflow must be accessible
> before it can be imported into another Galaxy.
> 
>
>
> As you can see I added the “New test Download” link.
> I have added and tested the function which gets me the information about
> the workflow I want correctly. For now it’s just a “hello world” string.
> When I don’t use load balancing I get the contents I want downloaded to
> the file correctly.
> However, when I activate load balancing, it only downloads an empty file.
> I can print the contents of the test download file to the galaxy log, but
> as I said nothing gets printed on the actual file.
>
> Is there some javascript code I also need to add for this functionality
> that I might be missing such that the download works with load balancing?
> As I mentioned I do get a proper download when load balancing is not
> activated. BTW, all other existing download links work properly with both
> load balancing and no load balancing.
>
> Thanks,
>
> Alex
>
>
>
>
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Re: [galaxy-dev] Loading tool config file

[Dannon Baker]

Hi Katherine,

This all happens in javascript these days, and it's unfortunately a little
harder to track down all the moving parts than it used to be when this was
all rendered serverside.  The client requests tool information (like which
parameters are necessary, etc) from the API, which it then renders using
the primary tool form found here:
https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/mvc/tool

This extends the form code found here:
https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/form

And individual element types (a select box, for example) can be found here:
https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/ui

Does this help?


On Fri, Jul 22, 2016 at 7:40 AM Peter Cock 
wrote:

> Sorry, I know relatively little about how Galaxy loads the tool XML
> files and turns this into the HTML pages. I've mostly searched
> the codebase with grep at the command line (also searching
> directly on GitHub works pretty well) trying to trace functionality
> when I was debugging something.
>
> Hopefully one of the Galaxy developers will be able to answer.
>
> Peter
>
>
> On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu wrote:
> >
> > No I'm really asking about which files in Galaxy, will load those
> > parameters on the screen. I believe you were the one to give me a link to
> > adding a new parameter type in Galaxy via the password parameter, but I
> > haven't quite been able to implement that. The two files I have changed
> so
> > far are basic.py and form_builder.py but using these two files it still
> only
> > loads a text parameter.
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Re: [galaxy-dev] activate authentication through LDAP using the auth_conf file

[Dannon Baker]

There's an open PR with a few build issues to build a Galaxy-side wheel for
python-ldap here: https://github.com/galaxyproject/starforge/pull/97, and
once that's resolved it should be automatically installed as a conditional
dependency the usual Galaxy way.

Until then, yeah, a workaround is to activate the virtualenv and pip
install it.  As you found out, to do that you'll need a few system packages
-- I had to install both libldap2-dev and libsasl2-dev on an ubuntu box
here to get it to build.  Good luck!

-Dannon

On Fri, Jul 22, 2016 at 7:07 AM Hans-Rudolf Hotz  wrote:

> Dear all
>
> I am looking into authentication through LDAP using the auth_conf file
> (we are currently using Apache to handle this). And it looks like, I am
> stuck at a very early step:
>
>
> I have started with a fresh checkout of release 16.04
> (git clone -b master https://github.com/galaxyproject/galaxy.git)
>
> some modifications in galaxy.ini (host, port) and:
>
> auth_config_file = config/auth_conf.xml
>
>
> I start galaxy, and I try to login. In the log file I get:
>
> galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741
> trans.app.config.auth_config_file: ./config/auth_conf.xml
> galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
> authenticate: email is hansrudolf.h...@fmi.ch
> galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
> authenticate: 
>
> This is what I expect...so far so good
>
> but further down, I get:
>
> galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP
> authenticate: could not load ldap module
>
>
> According to our sysadmin, "python-ldap" is installed on the machine
> (running Red Hat 7.2). But I assume, it has to be within the galaxy
> created virtual env, hasn't-it?
>
>
> Hence I have tried the following
>
>
> cd 
> . .venv/bin/activate
> pip install python-ldap
>
>
> Is this the right way to do it?
>
>
> Doing this, I have been running into the following error:
>
> Modules/errors.h:8:18: fatal error: lber.h: No such file or directory
> #include "lber.h"
>
>
> So I guess I have to tell my sysadmin to install "openldap-devel in
> order to have 'lber.h' on the system?
>
>
> Or do I have to do something else?
>
>
>
>
> Thank you very much for your help
> Hans-Rudolf
>
>
>
>
>
> --
>
>
>
> Hans-Rudolf Hotz, PhD
> Bioinformatics Support
>
> Friedrich Miescher Institute for Biomedical Research
> Maulbeerstrasse 66
> 4058 Basel/Switzerland
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Re: [galaxy-dev] tabular file displayed without tabs

[Dannon Baker]

You're welcome!

On Wed, Jun 22, 2016 at 4:49 PM Ryan G  wrote:

> That fixes it.  Thanks!
>
> On Tue, Jun 14, 2016 at 10:33 AM, Dannon Baker 
> wrote:
>
>> Ok, so it's definitely the column limit that's causing the unexpected
>> style-less display.  This currently isn't configurable per-galaxy (the plan
>> was to add more appropriate displays for many-columned files), but here's a
>> quick gist to show you how you might tweak this locally:
>>
>> https://gist.github.com/dannon/f67cccd16f9e8c8776a0032b11d1c5c7
>>
>> This would be really easy to turn into an app configuration setting in
>> galaxy.ini if it seems like something folks would want though I opted not
>> to do so originally to avoid configuration bloat for what seemed like a
>> very niche case.
>>
>> On Tue, Jun 14, 2016 at 10:23 AM Ryan G 
>> wrote:
>>
>>> No, it happens to all output from this particular tool.
>>>
>>> I do see a javascript warning in the console, 'The character encoding of
>>> a framed document was not declared.  The document may appear different if
>>> view without the document framing it.'
>>>
>>> The file does have 64 columns in it.  Is there a way to change Galaxy's
>>> default from 50 to something more?
>>>
>>>
>>>
>>> On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard 
>>> wrote:
>>>
>>>> Strange. Alright, a few questions then:
>>>>
>>>> * Is this the only file that this happens to? Do other outputs from
>>>> this tool produce the same sort of error?
>>>> * Do you see any javascript errors in the console when attempting the
>>>> viewing? (how to here: http://webmasters.stackexchange.com/a/77337)
>>>>
>>>> On Fri, May 27, 2016 at 12:42 PM, Ryan G 
>>>> wrote:
>>>>
>>>>> The format is listed as tabular when I view details.
>>>>>
>>>>> In fact, in the preview window in the History Pane, it recognizes
>>>>> there are columns and that the data is in fact tabular, but when
>>>>> displaying, this isn't the case.
>>>>>
>>>>>
>>>>>
>>>>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard <
>>>>> carlfeberh...@gmail.com> wrote:
>>>>>
>>>>>> Ok - if it's not zebra striped and it's word wrapping, then it's
>>>>>> somehow not displaying as tabular - you're correct.
>>>>>>
>>>>>> If you click on the 'View details' button of that dataset (the 'i'
>>>>>> with the circle around it shown when the dataset is expanded in the right
>>>>>> hand side of the 'Analyze Data' page), what does it list the 'Format' as?
>>>>>> 'tabular'? (This is also listed as 'Format' in the expanded view itself).
>>>>>>
>>>>>> On Mon, May 23, 2016 at 5:33 PM, Ryan G 
>>>>>> wrote:
>>>>>>
>>>>>>> Odd because I have another tabular file that is displayed with every
>>>>>>> other line highlighted and there is not word-wrapping on the file.  
>>>>>>> However
>>>>>>> the file that has the type tabular and displayed as text is word-wrapped
>>>>>>> with no lines highlighted.  I suspect its not actually recognized as
>>>>>>> tabular or is being overridden where.
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <
>>>>>>> carlfeberh...@gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi, Ryan
>>>>>>>>
>>>>>>>> Galaxy displays tabular data in the browser using a  tag. It
>>>>>>>> *sounds like* the behavior you see (columns losing space between one
>>>>>>>> another when narrowing the window and getting more space as you expand 
>>>>>>>> the
>>>>>>>> window) would reflect that.
>>>>>>>>
>>>>>>>> Carl
>>>>>>>>
>>>>>>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <
>>>>>>>> ngsbioinformat...@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> The file is an ou

Re: [galaxy-dev] tabular file displayed without tabs

[Dannon Baker]

Ok, so it's definitely the column limit that's causing the unexpected
style-less display.  This currently isn't configurable per-galaxy (the plan
was to add more appropriate displays for many-columned files), but here's a
quick gist to show you how you might tweak this locally:

https://gist.github.com/dannon/f67cccd16f9e8c8776a0032b11d1c5c7

This would be really easy to turn into an app configuration setting in
galaxy.ini if it seems like something folks would want though I opted not
to do so originally to avoid configuration bloat for what seemed like a
very niche case.

On Tue, Jun 14, 2016 at 10:23 AM Ryan G  wrote:

> No, it happens to all output from this particular tool.
>
> I do see a javascript warning in the console, 'The character encoding of a
> framed document was not declared.  The document may appear different if
> view without the document framing it.'
>
> The file does have 64 columns in it.  Is there a way to change Galaxy's
> default from 50 to something more?
>
>
>
> On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard 
> wrote:
>
>> Strange. Alright, a few questions then:
>>
>> * Is this the only file that this happens to? Do other outputs from this
>> tool produce the same sort of error?
>> * Do you see any javascript errors in the console when attempting the
>> viewing? (how to here: http://webmasters.stackexchange.com/a/77337)
>>
>> On Fri, May 27, 2016 at 12:42 PM, Ryan G 
>> wrote:
>>
>>> The format is listed as tabular when I view details.
>>>
>>> In fact, in the preview window in the History Pane, it recognizes there
>>> are columns and that the data is in fact tabular, but when displaying, this
>>> isn't the case.
>>>
>>>
>>>
>>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard 
>>> wrote:
>>>
 Ok - if it's not zebra striped and it's word wrapping, then it's
 somehow not displaying as tabular - you're correct.

 If you click on the 'View details' button of that dataset (the 'i' with
 the circle around it shown when the dataset is expanded in the right hand
 side of the 'Analyze Data' page), what does it list the 'Format' as?
 'tabular'? (This is also listed as 'Format' in the expanded view itself).

 On Mon, May 23, 2016 at 5:33 PM, Ryan G 
 wrote:

> Odd because I have another tabular file that is displayed with every
> other line highlighted and there is not word-wrapping on the file.  
> However
> the file that has the type tabular and displayed as text is word-wrapped
> with no lines highlighted.  I suspect its not actually recognized as
> tabular or is being overridden where.
>
>
> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <
> carlfeberh...@gmail.com> wrote:
>
>> Hi, Ryan
>>
>> Galaxy displays tabular data in the browser using a  tag. It
>> *sounds like* the behavior you see (columns losing space between one
>> another when narrowing the window and getting more space as you expand 
>> the
>> window) would reflect that.
>>
>> Carl
>>
>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G 
>> wrote:
>>
>>> The file is an output from a tool and in the tool's xml, its format
>>> is tabular.
>>>
>>>
>>>
>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>>> bjoern.gruen...@gmail.com> wrote:
>>>
 Hi Ryan,

 is it recognised as 'tabular'?

 Ciao,
 Bjoern

 Am 27.10.2015 um 04:42 schrieb Ryan G:
 > Hi - I have a tools that generates a tab-delimited text file as
 output.
 > when I click the eye icon to view the data, all the fields are
 compressed
 > as if there were no tabs.  If I expand the history view, the
 little preview
 > window shows the contents as tabbed.  I've verified that the
 spaces are
 > indeed '\t' tab characters.  Why would Galaxy not display this
 file as a
 > tab-delimited file?
 >
 >
 >
 > ___
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 > in your mail client.  To manage your subscriptions to this
 > and other Galaxy lists, please use the interface at:
 >   https://lists.galaxyproject.org/
 >
 > To search Galaxy mailing lists use the unified search at:
 >   http://galaxyproject.org/search/mailinglists/
 >

>>>
>>>
>>> ___
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>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>

>>

Re: [galaxy-dev] tabular file displayed without tabs

[Dannon Baker]

Sorry, I'm late to the thread -- one more question:
How many columns are in the file?

Galaxy will only display tabular datasets with fewer than 50 columns using
the 'fancy' display which also loads the file incrementally and renders on
demand.  For very 'wide' files, Galaxy defaults to using the original
tabular file display which is what you're seeing -- just serving the raw
data, or, in the case of large files, only the first 1MB.  There's an issue
on Github (or more likely, Trello, still) about creating a more suitable
"Matrix" view that'd work for files like these but that's work that has not
been done yet.

-Dannon


On Tue, May 31, 2016 at 8:18 AM Carl Eberhard 
wrote:

> Strange. Alright, a few questions then:
>
> * Is this the only file that this happens to? Do other outputs from this
> tool produce the same sort of error?
> * Do you see any javascript errors in the console when attempting the
> viewing? (how to here: http://webmasters.stackexchange.com/a/77337)
>
> On Fri, May 27, 2016 at 12:42 PM, Ryan G 
> wrote:
>
>> The format is listed as tabular when I view details.
>>
>> In fact, in the preview window in the History Pane, it recognizes there
>> are columns and that the data is in fact tabular, but when displaying, this
>> isn't the case.
>>
>>
>>
>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard 
>> wrote:
>>
>>> Ok - if it's not zebra striped and it's word wrapping, then it's somehow
>>> not displaying as tabular - you're correct.
>>>
>>> If you click on the 'View details' button of that dataset (the 'i' with
>>> the circle around it shown when the dataset is expanded in the right hand
>>> side of the 'Analyze Data' page), what does it list the 'Format' as?
>>> 'tabular'? (This is also listed as 'Format' in the expanded view itself).
>>>
>>> On Mon, May 23, 2016 at 5:33 PM, Ryan G 
>>> wrote:
>>>
 Odd because I have another tabular file that is displayed with every
 other line highlighted and there is not word-wrapping on the file.  However
 the file that has the type tabular and displayed as text is word-wrapped
 with no lines highlighted.  I suspect its not actually recognized as
 tabular or is being overridden where.


 On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <
 carlfeberh...@gmail.com> wrote:

> Hi, Ryan
>
> Galaxy displays tabular data in the browser using a  tag. It
> *sounds like* the behavior you see (columns losing space between one
> another when narrowing the window and getting more space as you expand the
> window) would reflect that.
>
> Carl
>
> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G 
> wrote:
>
>> The file is an output from a tool and in the tool's xml, its format
>> is tabular.
>>
>>
>>
>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>> bjoern.gruen...@gmail.com> wrote:
>>
>>> Hi Ryan,
>>>
>>> is it recognised as 'tabular'?
>>>
>>> Ciao,
>>> Bjoern
>>>
>>> Am 27.10.2015 um 04:42 schrieb Ryan G:
>>> > Hi - I have a tools that generates a tab-delimited text file as
>>> output.
>>> > when I click the eye icon to view the data, all the fields are
>>> compressed
>>> > as if there were no tabs.  If I expand the history view, the
>>> little preview
>>> > window shows the contents as tabbed.  I've verified that the
>>> spaces are
>>> > indeed '\t' tab characters.  Why would Galaxy not display this
>>> file as a
>>> > tab-delimited file?
>>> >
>>> >
>>> >
>>> > ___
>>> > Please keep all replies on the list by using "reply all"
>>> > in your mail client.  To manage your subscriptions to this
>>> > and other Galaxy lists, please use the interface at:
>>> >   https://lists.galaxyproject.org/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> >   http://galaxyproject.org/search/mailinglists/
>>> >
>>>
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>

>>>
>>
> ___
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Re: [galaxy-dev] Question: How to limit the number of dispatched jobs in Galaxy?

[Dannon Baker]

Hey George,

There sure is.  Let me know if this wiki page (
https://wiki.galaxyproject.org/Admin/Config/Jobs#Limiting_Job_Resource_Usage
)  doesn't have all the info you need and I can try to help more.

-Dannon

On Wed, May 25, 2016 at 4:04 PM George Weingart 
wrote:

> Hi
>
> Is there a way to  control the demand that Galaxy is putting on the server
> by limiting the number of jobs that will dispatch at a time ?
>
> Thanks!
> George Weingart PhD
> Huttenhower Lab
> Harvard School of Public Health
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Re: [galaxy-dev] Error when executing cleanup scripts

[Dannon Baker]

Hi Scott,

The quick fix is to source your virtualenv first and you should be good to
go.

-Dannon

On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi 
wrote:

> Hi all,
>
> I'm getting an error when executing the cleanup scripts in Galaxy 16.01.
> It appears the script is unable to import sqlalchemy, but my understanding
> is that Galaxy can't function without it, so I'm at a loss to explain.
> Here's the error I'm getting:
>
> $ sh scripts/cleanup_datasets/delete_userless_histories.sh
> Traceback (most recent call last):
>   File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in
> 
> import sqlalchemy as sa
> ImportError: No module named sqlalchemy
>
>
> We have relatively limited space on our storage server, so it's imperative
> that I be able to execute these scripts and be able to clean up deleted
> material. I welcome any suggestions.
>
> Best regards,
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
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Re: [galaxy-dev] galaxy.masthead.js change

[Dannon Baker]

Once you've changed the file, you'll need to rebuild the client.  Run 'make
client' from the root Galaxy directory and it should build your changes.

On Tue, May 17, 2016 at 8:20 AM Mohamed Kassam  wrote:

> Dear Aysam Guerler,
> thank you I find it, but I tried to change but I don't see any
> modification, don't know if it is this one or another javascript file that
> i have to change.
>
> Mohamed
>
> 2016-05-17 14:05 GMT+02:00 Aysam Guerler :
>
>> Hi Mohamed, the masthead file has been moved to
>> https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/layout/masthead.js
>> .
>>
>> On Tue, May 17, 2016 at 4:12 AM, Mohamed Kassam 
>> wrote:
>>
>>> Dear all,
>>> I would like to know which file replaced the galaxy.masthead.js file.
>>> Because I was putting in the banner the name and the logo of our local
>>> galaxy.
>>>
>>> Best regards,
>>>
>>>
>>> Mohamed
>>>
>>> ___
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>>>
>>
>>
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Re: [galaxy-dev] remote user CAS invalide session

[Dannon Baker]

This turned out to be a problem with how the maildomain was handled after a
recent fix to support API interactions bypassing remote user auth.

I'm working on a fix which you can follow and test here:
https://github.com/galaxyproject/galaxy/pull/2195

Thanks again for the report!

On Tue, Apr 19, 2016 at 8:25 AM, Dannon Baker 
wrote:

> Thank you for the report!  I'm able to reproduce this here on my local
> test install and will try to figure out what's going on and let you know
> when I have a fix.
>
> -Dannon
>
> On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC  > wrote:
>
>> Hi galaxy users,
>>
>> I just installed version 16.04 of galaxy. I can connect to galaxy with
>> remote user through CAS authentification but my session is invalidated, I
>> get this message in the history :
>> An error occurred while getting updates from the server. Please contact a
>> Galaxy administrator if the problem persists. Details
>>
>> In paster.log, I can see this :
>>
>> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged
>> in as 't...@company.fr' externally, but has a cookie as 'toto'
>> invalidating session
>>
>> and just after I can see :
>>
>> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged
>> in as 'toto' externally, but has a cookie as 't...@company.fr'
>> invalidating session
>>
>> It seems that variables remote_user_email and galaxy_session.user.email (
>> in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and
>> then set to login only... so the user login is not always the user email
>> address.
>>
>> In the config/galaxy.ini I set
>> remote_user_maildomain = company.fr
>> remote_user_header = HTTP_CAS_UID
>>
>> Can you tell me how to go through this ? I did not have this problem in
>> v16.01.
>>
>> Best regards
>>
>>
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>>
>
>
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Re: [galaxy-dev] remote user CAS invalide session

[Dannon Baker]

Thank you for the report!  I'm able to reproduce this here on my local test
install and will try to figure out what's going on and let you know when I
have a fix.

-Dannon

On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC 
wrote:

> Hi galaxy users,
>
> I just installed version 16.04 of galaxy. I can connect to galaxy with
> remote user through CAS authentification but my session is invalidated, I
> get this message in the history :
> An error occurred while getting updates from the server. Please contact a
> Galaxy administrator if the problem persists. Details
>
> In paster.log, I can see this :
>
> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged in
> as 't...@company.fr' externally, but has a cookie as 'toto' invalidating
> session
>
> and just after I can see :
>
> galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged in
> as 'toto' externally, but has a cookie as 't...@company.fr' invalidating
> session
>
> It seems that variables remote_user_email and galaxy_session.user.email (
> in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and
> then set to login only... so the user login is not always the user email
> address.
>
> In the config/galaxy.ini I set
> remote_user_maildomain = company.fr
> remote_user_header = HTTP_CAS_UID
>
> Can you tell me how to go through this ? I did not have this problem in
> v16.01.
>
> Best regards
>
>
>
>
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Re: [galaxy-dev] Missing dependency issue

[Dannon Baker]

Scott,

I'm not sure what's going on here, but maybe it'd be useful to try to run
the build by hand to see what's going on here?

cd /readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/

./configure


On Fri, Mar 11, 2016 at 8:25 AM, Scott Szakonyi 
wrote:

> Sorry, I was a bit premature. I did find the INSTALLATION.log file, but it
> only contains the original error message. I can't seem to find a config.log
> file anywhere.
>
> Thanks!
>
> Scott
>
> On Fri, Mar 11, 2016 at 8:19 AM, Scott Szakonyi  > wrote:
>
>> Hello Peter,
>>
>> Sadly, when I look in '../Galaxy/shed_tools/
>> toolshed.g2.bx.psu.edu/repos/iuc/package_readline_6_2/52d6f646b3b5/package_readline_6_2'
>> I don't see an installation log anywhere in the tree. I don't know what is
>> going on... I've always installed via the toolshed, so I don't think I've
>> done anything to mess it up through manual installations or so forth. I'll
>> keep looking, but if you or other folks on the list have additional
>> suggestions I would welcome them.
>>
>> Best,
>>
>> Scott
>>
>> On Thu, Mar 10, 2016 at 7:28 AM, Peter Briggs <
>> peter.bri...@manchester.ac.uk> wrote:
>>
>>> Hello Scott
>>>
>>> I don't have any insight into your specific problem with the readline
>>> package, however it might be worth looking for the INSTALLATION.log file
>>> from the tool install process.
>>>
>>> Assuming that this is the iuc version of package_readline_6_2 then you
>>> can try looking for it under
>>>
>>>
>>> .../tool_dependencies/readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/
>>>
>>> (the final subdirectory corresponds to the version hash so might be
>>> different for your installation).
>>>
>>> If present the INSTALLATION.log file should be in there and hopefully
>>> will give you some clues as to what the problem could be.
>>>
>>> HTH
>>>
>>> Best wishes
>>>
>>> Peter
>>>
>>> On 09/03/16 20:33, Scott Szakonyi wrote:
>>>
 Hello all,

 I'm having an issue with a missing dependency for readline 6.2. When I
 try to install or repair, I get the following error message:

 configure: error: in
 `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2':
 configure: error: cannot compute suffix of object files: cannot
 compile
 See `config.log' for more details.


 I've tried to locate the config.log file without success, so this is all
 I have to go on. Has anyone else encountered this sort of issue, and if
 so, how did you solve it?

 Thanks!

 --
 Scott B. Szakonyi
 Research Programmer

 *Center for Research Computing*
 107 Information Technology Center
 Notre Dame, IN 46556
 http://crc.nd.edu 


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>>> --
>>> Peter Briggs peter.bri...@manchester.ac.uk
>>> Bioinformatics Core Facility University of Manchester
>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>>
>>
>>
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>>
>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
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Re: [galaxy-dev] Error attempting to display contents of library (New data library)

[Dannon Baker]

Hi Juan,

I'm working on a few errors I've uncovered trying to track down your issue
here, but my hunch is you're hitting a different one.  The branch is here
if you want to try it:
https://github.com/dannon/galaxy/commits/library_errors

Do you have any non-ascii characters in a particular field that you've
noticed?  Perhaps in a dataset name, or filepath?  Barring that, can you
send me a screenshot of exactly what you're seeing prior to running into
the error?

-Dannon

On Sat, Mar 5, 2016 at 1:43 PM, Juan Vladimir de la Rosa Medina <
jvdelar...@hotmail.com> wrote:

> Hello to everybody,
>
>
>
> I’m trying to Access to my data files into a local instance of galaxy,
> installed in a virtual machine with Debian Jessie  8.2.0 (with Python 2.7.9
> installed), using the data libraries as administrator (I’m handling big
> data files). To do this task I have changed the option library_import_path
> into the config/galaxy.ini file to the path
> (“/home/jvdelarosa/Bioinformatica/BioDatos/”) where my files are located,
> as is explained in the Galaxy wiki section (“Uploading Files to a Data
> Library”).
>
>
>
> As administrator I can create a new data library, but when I’m trying to
> add datasets following the instructions explained in the section mentioned
> above, an error message is showed on the web browser.
>
>
>
> *“Error attempting to display contents of library (New data library):
> 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in
> range(128).”*
>
>
>
> I have to mention that I haven’t had any problem with other local galaxy
> instances I have installed in the past with the same O.S.
>
>
>
> I have been searching on the web about the same problem in galaxy with no
> success.
>
>
>
> Can anyone explain what’s happening with my local instance of galaxy and
> if there is any solution?
>
>
>
> A lot of thanks in advance.
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>
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Re: [galaxy-dev] quota api error

[Dannon Baker]

Fabien,

Thanks for the patch.  I've opened a PR applying it in
https://github.com/galaxyproject/galaxy/pull/1898.  I'm thinking we might
want to eventually refactor a little and add more general support for
Decimal serialization, perhaps in the 'safe_dumps' machinery in
galaxy.util.json, but this looks good to me for now.

On Tue, Mar 8, 2016 at 12:42 PM, Fabien Mareuil  wrote:

> Hi Dannon,
>
> I got this error with a detail view (/api/quotas/f597429621d6eb2b) when
> the quota has associated users with a disk usage different of 0,
> total_disk_usage in the user dictionary is a Decimal object and is not
> serializable.
> I worked on it this afternoon, it's possible to correct it just by adding
> the key 'total_disk_usage' in the value_mapper of the show method of
> QuotaAPIController class like the show method of UserAPIController class.
> I join a patch for the quota.py file with this email
> I can propose a pull request if you want.
>
>
> Best,
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris, France
>
>
>
> Le 08/03/2016 16:24, Dannon Baker a écrit :
>
> Hi Fabien,
>
> I'm having trouble reproducing this error on my side.  In the trace it
> looks like the error is being thrown at the collection view (/api/quotas)
> and not the detail view (/api/quotas/f597429621d6eb2b or the like).  Is
> that true?
>
> Can you show me the exact configuration of this quota in the admin panel?
>
> On Tue, Mar 8, 2016 at 8:10 AM, Fabien Mareuil 
> wrote:
>
>> Hi,
>>
>> We got an error when we used API to see a quota detail, we get the
>> following traceback:
>>
>> 157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas HTTP/1.1"
>> 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:44.0) Gecko/20100101
>> Firefox/44.0"
>> galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273 Uncaught
>> exception in exposed API method:
>> Traceback (most recent call last):
>>   File ".../lib/galaxy/web/framework/decorators.py", line 142, in
>> decorator
>> rval = dumps( rval, indent=4, sort_keys=True )
>>   File ".../lib/galaxy/util/json.py", line 65, in safe_dumps
>> dumped = json.dumps( *args, allow_nan=False, **kwargs )
>>   File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
>> **kw).encode(obj)
>>   File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
>> chunks = list(self.iterencode(o))
>>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
>> for chunk in self._iterencode_dict(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
>> _iterencode_dict
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 306, in _iterencode
>> for chunk in self._iterencode_list(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 204, in
>> _iterencode_list
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
>> for chunk in self._iterencode_dict(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
>> _iterencode_dict
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
>> for chunk in self._iterencode_dict(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
>> _iterencode_dict
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode
>> for chunk in self._iterencode_default(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 323, in
>> _iterencode_default
>> newobj = self.default(o)
>>   File "/usr/lib64/python2.6/json/encoder.py", line 344, in default
>> raise TypeError(repr(o) + " is not JSON serializable")
>> TypeError: Decimal('856488698767') is not JSON serializable
>>
>> json can't serialize Decimal object.
>> I tested it with simplejson and it works.
>> An other solution is to convert the Decimal object to a float before the
>> dumps.
>>
>> Thanks a lot for your help
>> Best regards,
>>
>> --
>> Fabien Mareuil | Centre d'Informatique pour la Biologie
>

Re: [galaxy-dev] Error installing from main toolshed

[Dannon Baker]

Hi Anmol,

It's a known temporary issue that we're working on right now.  Should be
resolved shortly.

-Dannon

On Wed, Mar 9, 2016 at 8:49 AM, Anmol Hemrom  wrote:

> Hi,
>
> I am getting error " HTTPError: HTTP Error 500: Internal Server Error"
> while installing tools from the main toolshed. I tried from different
> galaxy instances and got the same error.
>
> I have tried to export revision of a tool, that too threw the same error.
>
> Is it a temporary issue with main toolshed?  The testtoolshed is not
> working as well.
>
> Thanks
> Anmol
>
>
>
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] quota api error

[Dannon Baker]

Hi Fabien,

I'm having trouble reproducing this error on my side.  In the trace it
looks like the error is being thrown at the collection view (/api/quotas)
and not the detail view (/api/quotas/f597429621d6eb2b or the like).  Is
that true?

Can you show me the exact configuration of this quota in the admin panel?

On Tue, Mar 8, 2016 at 8:10 AM, Fabien Mareuil  wrote:

> Hi,
>
> We got an error when we used API to see a quota detail, we get the
> following traceback:
>
> 157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas HTTP/1.1"
> 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:44.0) Gecko/20100101
> Firefox/44.0"
> galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273 Uncaught
> exception in exposed API method:
> Traceback (most recent call last):
>   File ".../lib/galaxy/web/framework/decorators.py", line 142, in decorator
> rval = dumps( rval, indent=4, sort_keys=True )
>   File ".../lib/galaxy/util/json.py", line 65, in safe_dumps
> dumped = json.dumps( *args, allow_nan=False, **kwargs )
>   File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
> **kw).encode(obj)
>   File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
> chunks = list(self.iterencode(o))
>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
> for chunk in self._iterencode_dict(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
> _iterencode_dict
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 306, in _iterencode
> for chunk in self._iterencode_list(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 204, in
> _iterencode_list
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
> for chunk in self._iterencode_dict(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
> _iterencode_dict
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
> for chunk in self._iterencode_dict(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
> _iterencode_dict
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode
> for chunk in self._iterencode_default(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 323, in
> _iterencode_default
> newobj = self.default(o)
>   File "/usr/lib64/python2.6/json/encoder.py", line 344, in default
> raise TypeError(repr(o) + " is not JSON serializable")
> TypeError: Decimal('856488698767') is not JSON serializable
>
> json can't serialize Decimal object.
> I tested it with simplejson and it works.
> An other solution is to convert the Decimal object to a float before the
> dumps.
>
> Thanks a lot for your help
> Best regards,
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris, France
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] UnicodeDecodeError with 16.01

[Dannon Baker]

Ok, glad it's working for you now, but just swapping to English isn't the
long term solution I'd want to recommend :)

I had started some work on this a little while ago with Bjoern in
https://github.com/dannon/galaxy/commit/f9c3890135758a37c78aa18fe8b100be5895e67b,
but I wasn't particularly happy with that brute-force approach.  I'll
follow up on this, though, and make sure other locales also display
correctly in these grids --  I might go ahead and apply this for the time
being.

On Mon, Mar 7, 2016 at 10:18 AM, Anthony Bretaudeau <
anthony.bretaud...@inria.fr> wrote:

> Thanks all for your (very efficient) help!
> I added this to the env, and now it works:
>
> export LC_ALL=en_US.UTF-8
> export LANG=en_US.UTF-8
> export LANGUAGE=en_US.UTF-8
>
> It was fr_FR.UTF-8 before
>
> Anthony
>
>
> On 07/03/2016 16:15, Dannon Baker wrote:
>
> Before changing things, what's the output of 'locale'?
>
> You'll need to specify the .UTF-8 variant of that, though it need not be
> en_US.  Python's datetime functions use the configured locale, which when
> it isn't the UTF-8 variant, outputs incompatible encodings.
>
>
>
> On Mon, Mar 7, 2016 at 10:09 AM, Marius van den Beek <
> m.vandenb...@gmail.com> wrote:
>
>> Also it is sometimes necessary to remove outdated compiled mako.
>> By default this is in database/compiled_templates/
>>
>> On 7 March 2016 at 16:07, Björn Grüning < 
>> bjoern.gruen...@gmail.com> wrote:
>>
>>> Can you set your locale to something US UTF8 and restart your Galaxy.
>>>
>>> I guess this is happening because of some dates do are not in UTF-8.
>>>
>>> Am 07.03.2016 um 16:03 schrieb Anthony Bretaudeau:
>>> > Hi,
>>> > On our prod server that we udated to 16.01, I get this error when
>>> trying
>>> > to access the list of saved histories...
>>> > Do you see what's happening?
>>> > Anthony
>>> >
>>> >
>>> > URL: https://galaxy.genouest.org/history/list
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>>> > line 151 in __call__
>>> >   app_iter = self.application(environ, sr_checker)
>>> > File
>>> >
>>> '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py',
>>> > line 85 in __call__
>>> >   return self.application(environ, start_response)
>>> > File
>>> >
>>> '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
>>> > line 640 in __call__
>>> >   return self.application(environ, start_response)
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in
>>> > __call__
>>> >   return self.handle_request( environ, start_response )
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in
>>> > handle_request
>>> >   body = method( trans, **kwargs )
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66
>>> > in decorator
>>> >   return func( self, trans, *args, **kwargs )
>>> > File
>>> > '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py',
>>> > line 325 in list
>>> >   return self.stored_list_grid( trans, status=status, message=message,
>>> > **kwargs )
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line
>>> > 309 in __call__
>>> >   kwargs=kwargs )
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in
>>> > fill_template
>>> >   return self.fill_template_mako( filename, **kwargs )
>>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in
>>> > fill_template_mako
>>> >   return template.render( **data )
>>> > File
>>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py',
>>> > line 445 in render
>>> >   return runtime._render(self, self.callable_, args, data)
>>> > File
>>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py',
>>> > line 829 in _render
>>> >   **_kwargs_for_callable(callable_, data))
>>> > File
>>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py',
>>> > line 864 in _render_context
>>> >   _exec_templ

Re: [galaxy-dev] UnicodeDecodeError with 16.01

[Dannon Baker]

Before changing things, what's the output of 'locale'?

You'll need to specify the .UTF-8 variant of that, though it need not be
en_US.  Python's datetime functions use the configured locale, which when
it isn't the UTF-8 variant, outputs incompatible encodings.



On Mon, Mar 7, 2016 at 10:09 AM, Marius van den Beek  wrote:

> Also it is sometimes necessary to remove outdated compiled mako.
> By default this is in database/compiled_templates/
>
> On 7 March 2016 at 16:07, Björn Grüning  wrote:
>
>> Can you set your locale to something US UTF8 and restart your Galaxy.
>>
>> I guess this is happening because of some dates do are not in UTF-8.
>>
>> Am 07.03.2016 um 16:03 schrieb Anthony Bretaudeau:
>> > Hi,
>> > On our prod server that we udated to 16.01, I get this error when trying
>> > to access the list of saved histories...
>> > Do you see what's happening?
>> > Anthony
>> >
>> >
>> > URL: https://galaxy.genouest.org/history/list
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>> > line 151 in __call__
>> >   app_iter = self.application(environ, sr_checker)
>> > File
>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py',
>> > line 85 in __call__
>> >   return self.application(environ, start_response)
>> > File
>> >
>> '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
>> > line 640 in __call__
>> >   return self.application(environ, start_response)
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in
>> > __call__
>> >   return self.handle_request( environ, start_response )
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in
>> > handle_request
>> >   body = method( trans, **kwargs )
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66
>> > in decorator
>> >   return func( self, trans, *args, **kwargs )
>> > File
>> > '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py',
>> > line 325 in list
>> >   return self.stored_list_grid( trans, status=status, message=message,
>> > **kwargs )
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line
>> > 309 in __call__
>> >   kwargs=kwargs )
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in
>> > fill_template
>> >   return self.fill_template_mako( filename, **kwargs )
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in
>> > fill_template_mako
>> >   return template.render( **data )
>> > File
>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py',
>> > line 445 in render
>> >   return runtime._render(self, self.callable_, args, data)
>> > File
>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py',
>> > line 829 in _render
>> >   **_kwargs_for_callable(callable_, data))
>> > File
>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py',
>> > line 864 in _render_context
>> >   _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
>> > File
>> > '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py',
>> > line 890 in _exec_template
>> >   callable_(context, *args, **kwargs)
>> > File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line
>> > 61 in render_body
>> >   __M_writer(unicode(next.body()))
>> > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py',
>> > line 79 in render_body
>> >   __M_writer(unicode(self.load()))
>> > File
>> > '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py',
>> > line 53 in render_load
>> >   __M_writer(unicode(parent.load( embedded=embedded, insert=insert )))
>> > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py',
>> > line 107 in render_load
>> >   __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded,
>> > insert=insert ) ) ))
>> > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py',
>> > line 293 in render_get_grid_config
>> >   value = column.get_value( trans, grid, item )
>> > File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line
>> > 374 in get_value
>> >   return escape(value)
>> > UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1:
>> > ordinal not in range(128)
>> >
>> > ___
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >  https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >  http://galaxyproject.org/search/mailinglists/
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the u

Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[Dannon Baker]

I haven't seen this before but did a little googling.  What version is your
ansible installation?   If it's a little bit older, (
https://github.com/ansible/ansible/issues/5412) might be what you're seeing.

It's a bit of a long read, but it looks like reinstalling or updating your
ansible (or installing a new one in a fresh virtualenv for isolation)
should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge  wrote:

> Hi, all,
>
>
>
> Sorry to bother you again. I am trying to install tools using the script.
> I have downloaded the playbook, but stuck here:
>
>
>
> [galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml
> -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
>
> ERROR: pip is not a legal parameter of an Ansible Play
>
>
>
> I did not find anything related on the Galaxy search either. Any help will
> be appreciated.
>
>
>
> The web Admin interface only allows tool installation one by one. I wish
> it allows batch installation there.
>
>
>
> Thanks,
>
> Bill
>
>
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>
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Re: [galaxy-dev] AssertionError: there is no script for 130 version

[Dannon Baker]

Hey Bill,

The only time I've seen this is when switching from (for example) tip of
the 'dev' brach of Galaxy over to 16.01, 15.10, or some other stable
release.

Basically, sqlalchemy_migrate sees the 0130_change_pref_datatype.pyc (or
some other one) and thinks a version should exist.

The easiest fix for this is something like:  `find . -name "*.pyc"
-delete`, executed from your galaxy root directory.

-Dannon


On Thu, Feb 25, 2016 at 3:50 PM, William Ge  wrote:

> Hi, all,
>
>
>
> I  am new to Galaxy. The following error was encountered when I tried to
> run Galaxy after getting PostgreSQL up:
>
>
>
> File
> "/home/galaxy/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg/migrate/versioning/version.py",
> line 204, in script
>
> "There is no script for %d version" % self.version
>
> AssertionError: There is no script for 130 version
>
>
>
> I searched the lists and forums, but have not found any message. Anyone
> can give some hits?
>
>
>
> I’m running this on CentOS 6.7, virtual environment, python2.6, PostgresQL
> 8.4.20.
>
>
>
> Thanks in advance!
>
>
>
> Bill
>
>
>
> ___
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Re: [galaxy-dev] Collapse tool panel and history panel

[Dannon Baker]

Sure, I can help.  Which version of Galaxy are you currently running?  I
didn't check the history very well and the fix I suggested will work for
the forthcoming 16.01 release (or current dev branch), but not 15.10.


On Fri, Feb 19, 2016 at 8:32 AM, Makis Ladoukakis 
wrote:

> Hello Dannon,
>
> Sorry for asking but can you help me out a little bit with that? I
> searched in my galaxy directory in order to add those two lines you mention
> in the link but there is no galaxy/scripts/apps/analysis.js file and
> neither any file containing the string 'analysisPage.right.historyView'.
>
> Any advice?
>
> Thank you,
> Makis
> --
> Date: Mon, 28 Dec 2015 14:30:02 -0500
> Subject: Re: [galaxy-dev] Collapse tool panel and history panel
> From: dannon.ba...@gmail.com
> To: makis4e...@hotmail.com
> CC: galaxy-...@lists.bx.psu.edu
>
>
> Hi Makis,
>
> We've restructured much of the client code fairly recently.  Something
> like this should work for you now:
>
> https://gist.github.com/dannon/bd470d9c70019b07cb8b
>
>
> Sorry for the slow response!
>
> -Dannon
>
>
> On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis 
> wrote:
>
> Shamelessly bumping my own question... Does anyone have any ideas about
> collapsing the history and tool panel?
>
> Thank you,
> Makis Ladoukakis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu
> Date: Wed, 16 Dec 2015 13:41:19 +0200
> Subject: [galaxy-dev] Collapse tool panel and history panel
>
>
> Hello,
>
> Does anyone know how to start my Galaxy instance with the history panel
> and tool panel collapsed by default?
>
> I used to do it by editing the galaxy/templates/base/base_panels.mako
> script and adding
>
> *lp.do_toggle();*
>
> and
>
>
>
> *rp.do_toggle();*inside the if sections of *%if self.has_left_panel: *and *%if
> self.has_right_panel: *respectively but with my new installed instance
> this doesn't seem to work anymore.
>
> Any ideas anyone?
>
> Thank you,
> Makis Ladoukakis
>
>
>
>
> ___ Please keep
> all replies on the list by using "reply all" in your mail client. To manage
> your subscriptions to this and other Galaxy lists, please use the interface
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>
>
>
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[galaxy-dev] Python 2.6 Support

[Dannon Baker]

We're currently discussing when we should stop supporting Python2.6 and
it'd be useful to know how much this might impact local Galaxy
administrators.  Does anyone on the list have strong feelings or concerns
about this and want to weigh in?

Here's the issue on GitHub for more information and discussion:
https://github.com/galaxyproject/galaxy/issues/1596

Thanks!

Dannon
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Re: [galaxy-dev] Please terminate iGeneMap cluster

[Dannon Baker]

Hi Laura,

This is something we cannot do for you -- did you manage to get it done
from your end?

If not, you should be able to do so by simply going to the instance cloud
console (http:///cloud, in your browser) and selecting
"Terminate instance".  You can always confirm that termination by logging
into the AWS console and verifying the instance is no longer running.

Let me know if you need any help with this,

-Dannon

On Mon, Jan 4, 2016 at 11:47 AM Laura Song  wrote:

> Hi,
>
> I accidentally launched iGeneMap cluster. Please help me terminate it.
> Thanks.
>
> Laura
> ___
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Re: [galaxy-dev] security: brute force login

[Dannon Baker]

Hi Amogelang,

I'd recommend using a general purpose tool like fail2ban for this.  Here's
a quick getting started guide that might help if you're using nginx:
https://www.digitalocean.com/community/tutorials/how-to-protect-an-nginx-server-with-fail2ban-on-ubuntu-14-04

-Dannon

On Mon, Jan 4, 2016 at 2:13 PM, Raphenya, Amogelang 
wrote:

> Hi All,
>
> How can I prevent brute force login attack on the login page?
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Collapse tool panel and history panel

[Dannon Baker]

Hi Makis,

We've restructured much of the client code fairly recently.  Something like
this should work for you now:

https://gist.github.com/dannon/bd470d9c70019b07cb8b


Sorry for the slow response!

-Dannon


On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis 
wrote:

> Shamelessly bumping my own question... Does anyone have any ideas about
> collapsing the history and tool panel?
>
> Thank you,
> Makis Ladoukakis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu
> Date: Wed, 16 Dec 2015 13:41:19 +0200
> Subject: [galaxy-dev] Collapse tool panel and history panel
>
>
> Hello,
>
> Does anyone know how to start my Galaxy instance with the history panel
> and tool panel collapsed by default?
>
> I used to do it by editing the galaxy/templates/base/base_panels.mako
> script and adding
>
> *lp.do_toggle();*
>
> and
>
>
>
> *rp.do_toggle();*inside the if sections of *%if self.has_left_panel: *and *%if
> self.has_right_panel: *respectively but with my new installed instance
> this doesn't seem to work anymore.
>
> Any ideas anyone?
>
> Thank you,
> Makis Ladoukakis
>
>
>
>
> ___ Please keep
> all replies on the list by using "reply all" in your mail client. To manage
> your subscriptions to this and other Galaxy lists, please use the interface
> at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use
> the unified search at: http://galaxyproject.org/search/mailinglists/
>
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>
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Re: [galaxy-dev] INIT script for Ubuntu

[Dannon Baker]

Hi Mic,

The name of galaxy's default configuration file changed a while back (from
universe_wsgi.ini to galaxy.ini) but there is no functional difference.
Edit your copy of galaxy.ini the same way you see the tutorial changing
universe_wsgi.ini and you should be good to go.

-Dannon

On Fri, Dec 18, 2015 at 8:10 PM, Mic  wrote:

> HI Keith,
> Thank you for the links. In both links they use *universe_wsgi.ini*, but
> I am using *galaxy.ini*. Do I have to change to* universe_wsgi.ini *and
> does it has any advantages over *galaxy.ini*?
>
> Thank you in advance.
>
> Best wishes,
>
> Mic
>
> On Sat, Dec 19, 2015 at 1:51 AM, Suderman Keith 
> wrote:
>
>> Hi Mic,
>>
>> I based my startup script on the ones found here:
>>
>> 1.
>> https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
>> 2. http://simison.com/brian/GalaxyAdmin_notes.html
>>
>> HTH,
>> Keith
>>
>> > On Dec 17, 2015, at 5:54 PM, Mic  wrote:
>> >
>> > Hello,
>> > Where could I find INIT script for Ubuntu (14.04) and how to set is up?
>> >
>> > Thank you in advance.
>> >
>> > Mic
>> > ___
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >  https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >  http://galaxyproject.org/search/mailinglists/
>>
>>
>
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>
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Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

[Dannon Baker]

You're currently seeing 91% usage?  I just checked again and your disk
calculation should have been up to date (the recalc procedure did not
change anything), and I'm seeing 50% usage on your account.

On Tue, Dec 1, 2015 at 3:45 AM, Felix Mayr  wrote:
> The login emailaddress I use is felix.m...@gmail.com.
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
>
> Dear Galaxy dev,
>
> I have two problems, which might be related to each other.
>
> 1) For a long time already, I continuously have ‘left over’ data allocation
> after deleting and purging histories. Someone from your team has repeatedly
> resolved that problem, but it root of the problem still persists. I know
> have 91% allocation, when only having two histories of 67.48 and 59.45 GB.
> The fix for automatic recalculation doesn’t seem to work…?
>
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The
> problem: the SNP mapping plots shows the exact same mapping/plots of the
> SNPs. They can not be the same. What is not the problem: the input files, as
> they are different in size, first and last lines of the files, and they
> produce very different SNP mapping mutation tables. Therefore, I think there
> might be a problem that the workflow somehow uses the same intermediate file
> for generating the SNP mapping plots. I already re-uploaded and rerun the
> workflows in new histories multiple times, but the same result each time. I
> would upload and run another data set for which I already have SNP mapping
> plots to see whether I again get the same plots or not, but that is now not
> possible as I am close to the data quota.
>
> I hope you can help solve these problems.
>
> All best,
>
> Felix
>
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
>
>
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Re: [galaxy-dev] Set Galaxy as server

[Dannon Baker]

Hi,

There's a tutorial here that should hopefully help:
https://wiki.galaxyproject.org/Admin/GetGalaxy

Let us know if anything goes wrong, and we can try to help.  I'm not sure
which problems you may have had with Centos7, but please reply to the list
and we may be able to help out.

-Dannon

On Mon, Nov 9, 2015 at 11:26 AM Djurdjevic, Marija <
marija.durde...@medunigraz.at> wrote:

> Dir Sir/Madam,
>
>
>
> I am working in the Center for Medical Research and my new task is to
> establish Galaxy as server. Could you be so kind to give me some basic
> instruction regarding the Linux distribution which is the most suitable and
> stable for Galaxy? I already tried with Centos 7 and Virtual Box, but it
> wasn’t successful. Is there any good tutorial to follow during setting up?
>
>
>
> Thank you in advance.
>
> Kind regards,
>
>
>
> *Mag. Marija Đurđević*
>
> Core Facility Computational Bioanalytics
>
>
>
> Medical University of Graz
>
> Center for Medical Research
>
> Stiftingtalstraße 24, A-8010 Graz
>
> Austria
>
>
>
> Phone: +43 316/385-73024
>
> Fax:+43 316/385-73009
>
>
>
> Email: marija.djurdje...@klinikum-graz.at
>
>
>
> Web: https://zmf.medunigraz.at/
>
>
>
>
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Re: [galaxy-dev] email activation setting failed

[Dannon Baker]

Per the error message 'Temporary failure in name resolution', it sounds
like your server was unable to locate smtp.gmail.com.  Can you verify the
server does have the ability to connect to this machine and send email?

This may help:
https://stackoverflow.com/questions/11988454/how-to-check-if-smtp-is-working-from-commandline-linux

If it's working, then just retry sending the activation email.

On Mon, Nov 9, 2015 at 5:06 AM Jun Fan  wrote:

> Hi all,
>
>
>
>  I am using smtp.gmail.com as the smtp server with gmail account. It
> worked perfectly fine in the past. Just this morning, I received an email
> reporting the issue of failing to receive the activation email. The error
> message from Galaxy is “This account has not been activated yet but we are
> unable to send the activation link. “ Similarly in the error report
> function, there is also an expected error: “An error occurred sending the
> report by email: [Errno-3] temporary failure in name resolution”. Any ideas
> of how to solve the issue?
>
>
>
> Best regards!
>
> Jun
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Re: [galaxy-dev] login problem (redirection to the login page)

[Dannon Baker]

Hi Floreline,

This sounds a lot like your cookie_path specified in galaxy.ini might be
incorrect.  Are you using a proxy (and the proxy_prefix) in galaxy?  Can
you share the following lines and settings from your galaxy.ini, including
any comments (#) on the lines?  They should be near the beginning of the
file.

# Define the proxy-prefix filter.

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

filter-with = proxy-prefix
cookie_path = /galaxy



On Mon, Nov 9, 2015 at 5:59 AM Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:

> Hi,
>
> I'm still stuck with my login issue. Here is some additional information :
> - when I log in, it seems the authentication works because I get no error
> in the log but I'm redirected to the login page.
> - I saw some detailed http exchanges during the authentication phase.
> Between the login and redirection the session cookie changes. I don't know
> why.
> - I try to log in without Apache with the same result.
> - one of my colleagues advised me to watch the third part cookie loss
> problems with iframe. But I use Firefox which enables third part cookie.
> - My problem seems to lie on the server side. Is there other cache than
> Firefox I should clear ?
>
> Thank,
> F.T
> Le 5 nov. 2015 18:16, "Floreline TOUCHARD" 
> a écrit :
>
>> Hi,
>>
>> I come back to you with some news of my login problem.
>> I delete my browser cache and cookies with no result.
>> I restart all my services (Apache, PostgreSQL, Galaxy) with no more
>> result.
>> I try to start fresh with my PostgreSQL database cluster (to clear all
>> the user information). But it didn't solve the problem. When I register
>> with a user name, I get :
>>
>> - on the browser side:
>> "Now logged in as @example.com.
>> Verification email has been sent to your email address. Please verify it
>> by clicking the activation link in the email.
>> Please check your spam/trash folder in case you cannot find the message.
>> Return to the home page."
>>
>> - on the server side :
>> "galaxy.util ERROR 2015-11-05 17:21:25,394 Mail is not configured for
>> this Galaxy instance.
>> galaxy.util INFO 2015-11-05 17:21:25,394 From nobody Thu Nov  5 17:21:25
>> 2015
>> Content-Type: text/plain; charset="us-ascii"
>> MIME-Version: 1.0
>> Content-Transfer-Encoding: 7bit
>> To: @example.com
>> From:
>> Subject: Galaxy Account Activation
>> Hello ,
>> In order to complete the activation process for @example.com
>> begun on 11/05/15 at ip:port, please click on the following link to verify
>> your account:
>> http://ip:port/activate?email=%40example.com
>> &activation_token=3285151b21c8f85590db0f0c1089110d934f2400
>> By clicking on the above link and opening a Galaxy account you are also
>> confirming that you have read and agreed to Galaxy's Terms and Conditions
>> for use of this service (None). This includes a quota limit of one account
>> per user. Attempts to subvert this limit by creating multiple accounts or
>> through any other method may result in termination of all associated
>> accounts and data.
>> Please contact us if you need help with your account at: None. You can
>> also browse resources available at: None.
>> More about the Galaxy Project can be found at galaxyproject.org
>> Your Galaxy Team"
>>
>>
>> I get a new entry in the galaxy_user table (PostgreSQl table) with "f" in
>> the activate field. which I find logical.
>> If I activate the account with the link, the value becomes "t". Still
>> logical.
>>
>> But I'm redirected to the welcome page after the login and there's only
>> the "login" and "register" options under the user tab.
>> I have no error on the server log.
>> For each connection attempt I can see this line :
>> "galaxy.auth.providers.localdb DEBUG 2015-11-05 17:31:04,681 User:
>> @example.com, LOCALDB: True
>> 10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "POST
>> /user/login?use_panels=False HTTP/1.1" 200 - "http://ip:port/user/login";
>> "Mozilla/5.0 (Windows NT 6.1; rv:39.0) Gecko/20100101 Firefox/39.0"
>> 10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "GET /root HTTP/1.1" 200 -
>> "http://ip:port/user/login?use_panels=False"; "Mozilla/5.0 (Windows NT
>> 6.1; rv:39.0) Gecko/20100101 Firefox/39.0"
>> 10.80.6.195 - - [05/Nov/2015:17:31:05 +0200] "GET /root/welcome HTTP/1.1"
>> 302 - "http://ip:port/root"; "Mozilla/5.0 (Windows NT 6.1; rv:39.0)
>> Gecko/20100101 Firefox/39.0"
>> "
>> Is it normal ?
>>
>> My postgreSQl database seems to work fine.
>> It doesn't come from a browser cache issue (I clear mine and I try to
>> login to Galaxy with another computer on the same network).
>> Or are there other caches I should be aware of ?
>> Is there another way to get an operational application ? And where did
>> this issue come from ? I'm only testing the application but it surprises me
>> since I had a working instance for few months.
>>
>> Thanks in advance,
>> F.T
>>
>> 2015-11-04 16:44 GMT+01:00 Floreline TOUCHARD <
>> floreline.touch...@gmail.com>:
>>
>>> Update :
>>> When I clic sever

Re: [galaxy-dev] URGENT HELP!

[Dannon Baker]

It looks like the Galaxy server was downgraded relative the database.  Do
you know how this may have happened?

It also looks like this instance is probably quite a bit out of date, in
any event, so I'd be hesitant to give advice recommending a major upgrade
given the current state of things.  I'd say you should really get in touch
with the Galaxy Admin prior to trying much.

Is using a cloud instance for the training an option?


On Thu, Oct 29, 2015 at 11:44 AM Ali Al-Shahib 
wrote:

> Hi all
>
> I am due to give galaxy training tomorrow and the Galaxy server has gone
> down.  Our galaxy admin is travelling and not responding and I appreciate a
> quick response to this issue.
>
> When I run galaxy_restart.sh I get the following error in web0.pid:
>
> migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config:
> {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
> 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
>
> lib/galaxy/model/migrate
>
> galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg
> successfully loaded for postgresql dialect
>
> Traceback (most recent call last):
>
>   File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
>
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>
>   File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
>
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
> ).get( '__file__', None ), self.config.database_engine_options, app=self )
>
>   File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line
> 104, in create_or_verify_database
>
> % ( db_schema.version, migrate_repository.versions.latest, config_arg
> ) )
>
> Exception: Your database has version '124' but this code expects version
> '115'.  Please backup your database and then migrate the schema by running
> 'sh manage_db.sh upgrade'.
>
>
> --
>
>
>
> I did then try to do sh manage_db.sh downgrade 115 but I got this error:
>
>
> Traceback (most recent call last):
>
>   File "./scripts/manage_db.py", line 62, in 
>
> main( repository=repo, url=db_url )
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py",
> line 207, in main
>
> ret = command_func(**kwargs)
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
> line 202, in downgrade
>
> return _migrate(url, repository, version, upgrade=False, err=err,
> **opts)
>
>   File "", line 2, in _migrate
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py",
> line 159, in with_engine
>
> return f(*a, **kw)
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
> line 345, in _migrate
>
> changeset = schema.changeset(version)
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py",
> line 80, in changeset
>
> changeset = self.repository.changeset(database, start_ver, version)
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
> line 225, in changeset
>
> changes = [self.version(v).script(database, op) for v in versions]
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
> line 189, in version
>
> return self.versions.version(*p, **k)
>
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py",
> line 140, in version
>
> return self.versions[VerNum(vernum)]
>
> KeyError: 
>
>
> Any help asap will be greatly appreciated.
>
>
> Ali
>
> **
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Re: [galaxy-dev] using Bioblend with external authentication

[Dannon Baker]

My guess is that it has to do with the prefix there.  Is the Galaxy API at
galaxy-dev.fmi.ch/galaxy/api or galaxy-dev.fmi.ch/api?

On Thu, Oct 22, 2015 at 6:41 AM Hans-Rudolf Hotz  wrote:

> Hi
>
> We would like to start using BioBlend on our production servers (which
> use external authentication) as well.
>
> We have changed the apache conf file by adding
>
>   
>   Satisfy Any
>   Allow from all
>   
>
>
>
> Nevertheless, we still get the following error, when using one of the
> example scripts:
>
>
> $ python list_data_libraries.py galaxy-dev.fmi.ch ***
> Initiating Galaxy connection
> Retrieving Data Library list
> Traceback (most recent call last):
>File "list_data_libraries.py", line 23, in 
>  libraries = gi.libraries.get_libraries()
>File
>
> "//lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/libraries/__init__.py",
> line 216, in get_libraries
>  libraries = Client._get(self, deleted=deleted)
>File
>
> "//lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/client.py",
> line 147, in _get
>  raise ConnectionError(msg)
> bioblend.galaxy.client.ConnectionError: GET: error 401: ' PUBLIC "-//IETF//DTD HTML 2.0//EN">\n\n401
> Authorization Required\n\nAuthorization
> Required\nThis server could not verify that you\nare authorized
> to access the document\nrequested.  Either you supplied the
> wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t
> understand how to supply\nthe credentials
> required.\n', 0 attempts left: None
> $
>
>
> Is there anything else we need to change in the conf file, or do we have
> to do something different?
>
>
>
> Thank you very much for any help with this
> Hans-Rudolf
>
>
>
> --
>
>
>
> Hans-Rudolf Hotz, PhD
> Bioinformatics Support
>
> Friedrich Miescher Institute for Biomedical Research
> Maulbeerstrasse 66
> 4058 Basel/Switzerland
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Re: [galaxy-dev] updated eggs needed for OS X El Capitan compatibility

[Dannon Baker]

Hi Wolfgang,

Thanks for the extensive testing!  I hadn't noticed this since I was using
a brew-installed python in a virtualenv, but I can confirm that this is
broken with the new OSX system python.  I'll build and test a few updated
eggs now.

-Dannon

On Mon, Oct 12, 2015 at 6:18 AM Wolfgang Maier <
wolfgang.ma...@biologie.uni-freiburg.de> wrote:

> Hi,
>
> today, there was a complaint on the Galaxy Biostar forum that Galaxy
> fails to start under the new OS X El Capitan
> (https://biostar.usegalaxy.org/p/14492/).
>
> I had noticed this last week already, and that post prompted me to
> investigate the problem in more detail.
> The result (now checked on our own Galaxy instance) is that
> compatibility with El Capitan requires updates to two eggs - amqp and
> kombu - in the sense that, at least, you can start Galaxy after fixing
> these two. I haven't checked to see if there are additional run time
> problems.
>
> Hope that information helps,
> Wolfgang
>
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Re: [galaxy-dev] Need urgent help: ItemOwnershipException: History is not owned by user

[Dannon Baker]

Glad you figured it out!  So a page served via https is generating links
for http references that should have been https?

On Mon, Sep 21, 2015 at 5:15 PM, Zuzanna K. Filutowska <
plat...@man.poznan.pl> wrote:

> Dnia 2015-09-21, pon o godzinie 13:29 -0400, Carl Eberhard pisze:
> > I'm stumped:
> >   * I'm not sure how that url
> > ("
> http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c184a9/contents";)
> could have been formed
> >   * Calling that link from a local galaxy results in 'No route
> > for' when the error is an api authentication 403
> > Maybe it's possible that an authentication error is
> > confounding/combining with a client error?
> >
> >
> >
> > Zuzanna, can you:
> >   * tell us what version of Galaxy you're using?
> >   * open a javascript console on the history/view_multiple page
> > and see what it says 'galaxy_conf.root' equals?
> >
>
> It took me 13 hours to figure it out but it seems that the problem was
> caused by this:
> RequestHeader set X-URL-SCHEME https
>
> inside my .
>
> I have set it according to the docs:
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
> as I use apache proxy with SSL, but without it the proxy works fine, as
> well as uploads and history import. Maybe this case is worth mentioning
> in the docs.
>
> --
>
> Pozdrawiam,
>
> --
> Zuzanna K. Filutowska, HPC Systems Administrator
> Poznan Supercomputing and Networking Center
> Institute of Bioorganic Chemistry Polish Academy of Sciences
> Seize the day boys! Make your lifes extraordinary! --John Keating
>
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Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

[Dannon Baker]

Thanks.  Can you specify exactly which release (or even the exact
changeset) of the galaxy revision you're running, and what encoding the
database is currently set to?  I've reproduced the error with the latest
galaxy release, mysql 5.6.26 (utf8 encoding) and will get a fix out
shortly, but I want to make sure I'm testing your situation as well.

On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders <
m.end...@german-seed-alliance.de> wrote:

> It was the name of the File:
>
>
>
> Blühzeitpunkt.txt
>
>
>
> (for example)
>
>
>
> *Von:* Dannon Baker [mailto:dannon.ba...@gmail.com]
> *Gesendet:* Thursday, September 10, 2015 4:12 PM
> *An:* Matthias Enders 
> *Cc:* galaxy-dev@lists.galaxyproject.org
> *Betreff:* Re: [galaxy-dev] Fatal Error while uploading a File with
> special Characters
>
>
>
> You should definitely not have to purge a user to fix this (not that it
> should happen in the first place).  Was it the file with special
> characters, or the name of the file?
>
>
>
>
>
>
>
> On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <
> m.end...@german-seed-alliance.de> wrote:
>
> Dear Galaxy Community,
>
> a User of our Galaxy Platform has produced a fatal error by uploading a
> file containing a German special character  (ä / ü / ö / ß). This resulted
> in the following status (only for the given user):
>
> - Upload was canceled: Status was "Failed Internal Server Error (500)"
> - All Histories were corrupt stating: "An error was encountered while
> loading the contents."
> - Tools can´t be used an stating (in Traceback):
> " UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5:
> invalid start byte"
> "Module weberror.evalexception.middleware:364 in respond"
>
>
> This totally destroyed to current user and we have had to purge him in
> order to get him back to work, even losing all his datasets & histories!
>
> We are using an MySQL database as a backend. Is the Encoding of this
> database the problem? If yes: Which encoding is used/supported by galaxy?
>
> Thanks in advance!
>
> Matthias
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Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

[Dannon Baker]

You should definitely not have to purge a user to fix this (not that it
should happen in the first place).  Was it the file with special
characters, or the name of the file?



On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <
m.end...@german-seed-alliance.de> wrote:

> Dear Galaxy Community,
>
> a User of our Galaxy Platform has produced a fatal error by uploading a
> file containing a German special character  (ä / ü / ö / ß). This resulted
> in the following status (only for the given user):
>
> - Upload was canceled: Status was "Failed Internal Server Error (500)"
> - All Histories were corrupt stating: "An error was encountered while
> loading the contents."
> - Tools can´t be used an stating (in Traceback):
> " UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5:
> invalid start byte"
> "Module weberror.evalexception.middleware:364 in respond"
>
>
> This totally destroyed to current user and we have had to purge him in
> order to get him back to work, even losing all his datasets & histories!
>
> We are using an MySQL database as a backend. Is the Encoding of this
> database the problem? If yes: Which encoding is used/supported by galaxy?
>
> Thanks in advance!
>
> Matthias
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Re: [galaxy-dev] External User Authenticaion

[Dannon Baker]

Do you have a way to verify the "HTTP_MAIL" header is actually being passed
through your proxy server?

The problem is that Galaxy still doesn't think it's receiving the expected
headers, so there isn't a good way that it can tell you more about what
might be going on.  If you're able to tweak Galaxy (using a test server)
and add a few logging statements the code, this would be good places to
check what's going on (print the `environ` dictionary associated with that
request, along with self.remote_user_header to see what Galaxy is actually
trying to use):

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49

-Dannon

On Thu, Sep 3, 2015 at 1:51 PM, Ryan G  wrote:

> It turns out our authentication system passes a header 'HTTP_MAIL' which
> contains the users email address.  In galaxy.ini, I have
>
> use_remote_user = True
> remote_user_header = HTTP_MAIL
>
> After restarting,Galaxy still gives the same error.
>
> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker 
> wrote:
>
>> Hi Ryan,
>>
>> It may be that Galaxy is looking for a different remote user header than
>> your proxy is setting.  I believe by default we look for HTTP_REMOTE_USER,
>> but this is configurable in galaxy.ini (so, you could set yours to
>> HTTP_USER there).  Let me know if this doesn't sort it out for you and we
>> can dig deeper!
>>
>> -Dannon
>>
>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G 
>> wrote:
>>
>>> Hi all - I'm trying to use external user authentication with Galaxy.
>>> The external authentication passes to Galaxy the username with the mail
>>> domain at HTTP_USER.
>>>
>>> In galaxy.ini, I enable:
>>> use_remote_user = True
>>>
>>>
>>> When I try to access Galaxy, I get the message:
>>> Galaxy is configured to authenticate users via an external method (such
>>> as HTTP authentication in Apache), but a username was not provided by the
>>> upstream (proxy) server. This is generally due to a misconfiguration in the
>>> upstream server.
>>>
>>> But nothing in paster.log indicating what the error is.
>>>
>>> How do I track this down?
>>>
>>>
>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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Re: [galaxy-dev] External User Authenticaion

[Dannon Baker]

Hi Ryan,

It may be that Galaxy is looking for a different remote user header than
your proxy is setting.  I believe by default we look for HTTP_REMOTE_USER,
but this is configurable in galaxy.ini (so, you could set yours to
HTTP_USER there).  Let me know if this doesn't sort it out for you and we
can dig deeper!

-Dannon

On Mon, Aug 31, 2015 at 3:42 PM, Ryan G  wrote:

> Hi all - I'm trying to use external user authentication with Galaxy.  The
> external authentication passes to Galaxy the username with the mail domain
> at HTTP_USER.
>
> In galaxy.ini, I enable:
> use_remote_user = True
>
>
> When I try to access Galaxy, I get the message:
> Galaxy is configured to authenticate users via an external method (such as
> HTTP authentication in Apache), but a username was not provided by the
> upstream (proxy) server. This is generally due to a misconfiguration in the
> upstream server.
>
> But nothing in paster.log indicating what the error is.
>
> How do I track this down?
>
>
>
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Re: [galaxy-dev] login problems when using a proxy and serving at a subdirectory

[Dannon Baker]

When I've seen similar behavior in the past, it's always that cookie_path
is incorrect.

On Thu, Aug 27, 2015 at 1:46 PM, John Chilton  wrote:

> Not really sure what is happening here, does your galaxy.ini file have
> the following sections:
>
> [filter:proxy-prefix]
> use = egg:PasteDeploy#prefix
> prefix = /galaxy
>
> [app:main]
>
> filter-with = proxy-prefix
> cookie_path = /galaxy
>
> If yes, it might be best to share nginx configuration and your galaxy
> logs when this occurs so we can see what routes Galaxy thinks are
> being accessed.
>
> -John
>
>
> On Thu, Aug 27, 2015 at 4:50 PM, Bernau, Christoph
>  wrote:
> > Dear all,
> >
> >
> >
> > I have a problem with configuring my galaxy instance with a proxy server
> > when I try to  serve at a subdirectory.
> >
> >
> >
> > I followed the description at
> > https://wiki.galaxyproject.org/Admin/Config/nginxProxy
> >
> >
> >
> > The basic configuration works just fine.
> >
> >
> >
> > When I use the procedure described in the section
> >
> > “serving galaxy at a subdirectory”, the proxying principally also works.
> >
> >
> >
> > However, when registered users try to log in to galaxy, galaxy will
> simply
> > directs them to the starting page (which I think is
> >
> > what normally happens after logging in) without displaying an error
> message.
> > Nonetheless, users do not have access to the functionalities which only
> > logged in users
> >
> > can use. E.g. each time they try to use the “workflows”-button they are
> told
> > to log in.
> >
> >
> >
> > Could you please provide any help on this issue?
> >
> >
> >
> > Cheers,
> >
> > Christoph
> >
> >
> > ___
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Re: [galaxy-dev] default value for param type "color"

[Dannon Baker]

Hi Wolfgang,

You should be able to set a default value for the color parameter by
including 'value' with an appropriate color value in the tag.  Something
like the following would default to red, for example:



-Dannon

On Fri, Aug 14, 2015 at 6:43 PM, Wolfgang Maier <
wolfgang.ma...@biologie.uni-freiburg.de> wrote:

> Hi,
>
> I've started to explore the relatively new "color" parameter type, which
> is not explained in the ToolConfigSyntax section of the Wiki yet.
>
> It's a pretty neat new feature, but I haven't found a way to specify a
> default color yet (the color selection is always set to a very light orange
> initially). Is this possible yet? If not I think it should really be added.
>
> Best,
> Wolfgang
>
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Re: [galaxy-dev] Security issues

[Dannon Baker]

Hi Scott,

Serious security problems should not be fixed via pull request - please
responsibly disclose these by e-mailing them (with or without patches) to
galaxy-...@lists.galaxyproject.org. The Galaxy core development team will
issue patches to public servers before announcing the issue to ensure there
is time to patch and highlight these fixes widely. We will provide you
credit for the discovery when publicly disclosing the issue.

-Dannon

On Tue, Aug 11, 2015 at 10:16 AM, Scott Szakonyi 
wrote:

> Hello all,
>
> In testing our servers for security vulnerabilities, we've detected some
> cross site scripting and SQL injection problem on our Galaxy server. Is
> that something that should be reported as a bug/problem? I did search the
> Trello board but didn't find any open security related items.
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
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Re: [galaxy-dev] Bug on current history when using prefix in galaxy input file

[Dannon Baker]

Interesting.  Can you clear your cache on firefox and try again?  Do you
see any errors in the web console?

On Wed, Jul 29, 2015 at 7:35 PM, Ata Roudgar  wrote:

>
> Hi Dannon,
>
> Thanks for reply. I did a test with other web browser and it seems that
> this problem persist only when I work with Firefox. With IE or Chrome the
> problem seems to be disappeared.
>
>
> Thanks again.
> Cheers,
> Ata
>
>
> On Wednesday 2015-07-29 16:25, Dannon Baker wrote:
>
>  Date: Wed, 29 Jul 2015 16:25:19
>> From: Dannon Baker 
>> To: Ata Roudgar 
>> Cc: "galaxy-dev@lists.galaxyproject.org" <
>> galaxy-dev@lists.galaxyproject.org>,
>>Franklin Bristow ,
>>Matthew Laird 
>> Subject: Re: [galaxy-dev] Bug on current history when using prefix in
>> galaxy
>>input file
>>
>>
>> Hi Ata,
>>
>> I'm a little stumped by this one, unable to replicate it here.  Out of
>> curiosity, does it work if you remove
>> the trailing slashes from your prefix and cookie_path (when set)?
>>
>> -Dannon
>>
>> On Wed, Jul 15, 2015 at 7:15 PM, Ata Roudgar  wrote:
>>
>>
>>  Hi,
>>
>>  I am using the most recent version of Galaxy. There seems to be a
>> bug in viewing the current
>>  (active) history when I use prefix in galaxy input file.
>>
>>  Here is the detail:
>>
>>  When I do not use prefix, e.g., in /config/galaxy.in :
>>
>>  prefix = /
>>  cookie_path = /
>>
>>  and run galaxy server, I can upload a file and I can see my uploaded
>> file in the current history
>>  even after I refresh the web browser (e.g., close and reopen the web
>> browser) which seems to be
>>  working fine. However when I use prefix, e.g. in /config/galaxy.in :
>>
>>  prefix = /galaxy-1/
>>  cookie_path = /galaxy-1/
>>
>>  then after I upload a file and refresh the browser I do not see the
>> uploaded file in the current
>>  (or active) history. It always shows me a new (clean history). This
>> is a problem because I get a
>>  error which seems to be related to the history when I attempt to run
>> any workflow.
>>
>>  Any idea where the problem should be?
>>
>>  Please note that I use external authentication but it shouldn't be
>> matter because it is working
>>  when the prefix is "/".
>>
>>  Thanks a lot,
>>  Cheers,
>>  Ata
>>
>>
>>  
>>  Ata Roudgar
>>  Research Computing
>>  WestGrid Site
>>  IT Services
>>  Simon Fraser University
>>  Burnaby, British Columbia
>>  Canada  V5A 1S6
>>
>>  phone: 778 782-8860
>>  fax:   778 782-4242
>>
>>  ___
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>>  in your mail client.  To manage your subscriptions to this
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>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>>
>>
> 
> Ata Roudgar
> Research Computing
> WestGrid Site
> IT Services
> Simon Fraser University
> Burnaby, British Columbia
> Canada  V5A 1S6
>
> phone: 778 782-8860
> fax:   778 782-4242
>
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Re: [galaxy-dev] Bug on current history when using prefix in galaxy input file

[Dannon Baker]

Hi Ata,

I'm a little stumped by this one, unable to replicate it here.  Out of
curiosity, does it work if you remove the trailing slashes from your prefix
and cookie_path (when set)?

-Dannon

On Wed, Jul 15, 2015 at 7:15 PM, Ata Roudgar  wrote:

>
>
> Hi,
>
> I am using the most recent version of Galaxy. There seems to be a bug in
> viewing the current (active) history when I use prefix in galaxy input file.
>
> Here is the detail:
>
> When I do not use prefix, e.g., in /config/galaxy.in :
>
> prefix = /
> cookie_path = /
>
> and run galaxy server, I can upload a file and I can see my uploaded file
> in the current history even after I refresh the web browser (e.g., close
> and reopen the web browser) which seems to be working fine. However when I
> use prefix, e.g. in /config/galaxy.in :
>
> prefix = /galaxy-1/
> cookie_path = /galaxy-1/
>
> then after I upload a file and refresh the browser I do not see the
> uploaded file in the current (or active) history. It always shows me a new
> (clean history). This is a problem because I get a error which seems to be
> related to the history when I attempt to run any workflow.
>
> Any idea where the problem should be?
>
> Please note that I use external authentication but it shouldn't be matter
> because it is working when the prefix is "/".
>
> Thanks a lot,
> Cheers,
> Ata
>
>
> 
> Ata Roudgar
> Research Computing
> WestGrid Site
> IT Services
> Simon Fraser University
> Burnaby, British Columbia
> Canada  V5A 1S6
>
> phone: 778 782-8860
> fax:   778 782-4242
>
> ___
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Re: [galaxy-dev] Problems installing pbs_python from scramble.

[Dannon Baker]

Hi Zuzanna,

You can temporarily relocate the 'pkg_resources.py' that ships with Galaxy
(and delete the corresponding .pyc file) to get around this error.  Let me
know if this doesn't work for you, though, and I can help debug some more.

We're hoping to swap to new dependency management code that should resolve
this error in a coming release.

-Dannon

On Wed, Jul 29, 2015 at 7:25 AM, Zuzanna K. Filutowska <
plat...@man.poznan.pl> wrote:

> Dnia 2015-07-29, śro o godzinie 12:35 +0200, Zuzanna K. Filutowska
> pisze:
>
> It is worth to add that I installed pip, and tried to install pbs_python
> using pip or easy_install and these seems to work fine.
>
> --
>
> Pozdrawiam,
>
> --
> Zuzanna K. Filutowska, HPC Systems Administrator
> Poznan Supercomputing and Networking Center
> Institute of Bioorganic Chemistry Polish Academy of Sciences
> Seize the day boys! Make your lifes extraordinary! --John Keating
>
> ___
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Re: [galaxy-dev] Setting up Galaxy without e-mail

[Dannon Baker]

Hi Raymond,

Regarding activation, you mean you set user_activation_on = True, right?
You can just leave 'user_activation_on = False', which is the default (and
the value if left commented), which will disable any requirement of having
a local SMTP server for user creation and won't validate the account.

If this instance is going to be a production server, I'd *strongly*
recommend just starting it right now with a Postgresql database.  Porting
data over is not something you'll want to have to deal with.

-Dannon

On Wed, Jul 29, 2015 at 5:40 AM, Raymond Wan  wrote:

> Dear all,
>
> I just started setting up a galaxy instance and I'm a bit stuck with
> user account activation without e-mail.  Is it possible to run Galaxy
> without an SMTP server set?
>
> For example, for the administrator user, I set:
>
> admin_users = 
>
> in galaxy.ini .  I'd also like to require login (i.e., require_login =
> True) but it seems that I can't do that from the outset.  That has to
> be False and allow_user_creation has to be True.
>
> Then I can create a user with the same account as above, who will then
> become an administrator.  But, the account has to be validated some
> how and I can't seem to figure out how to do that without enabling an
> SMTP server.
>
> Am I doing something that wasn't intended?  Perhaps I must have an
> SMTP server set?  Or are there other steps I should do to activate the
> administrator?  The web page
> https://wiki.galaxyproject.org/Admin/GetGalaxy makes it look easy...so
> I am concerned I'm doing it all wrong...
>
> Also, if this instance will be a production system some day, should I
> start using a database (Postgres or MySQL) right away and not bother
> with the default SQLite?  Otherwise, I will have to port the data
> over, which the documentation implies is not an easy thing to do...
>
> Thank you!
>
> Ray
> ___
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Re: [galaxy-dev] ERROR in Galaxy

[Dannon Baker]

Hi Stephanie,

Can you provide more details as to what you were trying to do when you
observed this error?

Thanks!

Dannon

On Mon, Jul 27, 2015 at 9:13 AM Stephanie Beck Roth <
stephanie.beckr...@mail.wvu.edu> wrote:

>  I have been receiving the following error for over an hour:
>
>  The server could not complete the request. Please contact the Galaxy
> Team if this error persists.
>
>  {
> "outputs": [],
> "implicit_collections": [],
> "jobs": [],
> "output_collections": []
> }
>
> 
>
> Stephanie R Beck Roth, PhD
>
> Assistant Professor of Mathematics
>
> Potomac State College of WVU
>
> 101 Fort Ave.
>
> Keyser, WV 26726
>
> (304) 788 – 7118
>
> stephanie.beckr...@mail.wvu.edu
>
>
>
> “If you come to a fork in the road, take it.”  ~ Yogi Berra
>
>
>  “Nothing will work unless you do.” ~Maya Angelou
>   ___
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Re: [galaxy-dev] Slow repsonses viewing histories

[Dannon Baker]

Hey Christian,

I used /scripts/db_shell.py and something like
https://gist.github.com/dannon/e71b7aa9546fcecf6e9e to reset problematic
BAM metadata.  Basically, it selects all the large metadata and completely
strips out the new overly large optional attributes, leaving required
attributes alone.  Once this is done, you can redetect metadata if you'd
like (with the limits we'd talked about set) and it should all work fine.

Let me know if you need more info, hopefully this helps!

-Dannon

On Fri, Jul 24, 2015 at 11:23 AM Christian Schudoma (TSL) <
christian.schud...@sainsbury-laboratory.ac.uk> wrote:

>  Hi Nate, all
>
> I would like to add my own version of the problem to this.
>
> I, or rather my (inherited) Galaxy instance (which should be running
> 15.05+, how do I find out?), have/s similar symptoms as Richard's did. In
> my case it only occurs to a single user and we are not able to execute the
> "Saved Histories" command any more. Galaxy will fail with
>
>
> Proxy Error
>
> The proxy server received an invalid response from an upstream server.
> The proxy server could not handle the request GET /history/list.
>
>
> Reason: Error reading from remote server
>
> Due to some problem with the psql-client I cannot find the potential
> perpetrators (my user has lots of bam files in various histories) and since
> he cannot switch histories, we cannot even update the metadata for his
> datasets. Is there a possibility to do that via the API?
>
> Any insight/help would be greatly appreciated!
>
> Cheers
> Christian
>
>
> On 08/07/15 21:04, Poole, Richard wrote:
>
>
>  I am having trouble right now with my own personal account on my
> production server. Grid refreshes are taking a huge amount of time (e.g.
> when viewing ‘saved histories’ or even generating the dataset list for a
> single history). My account is very full of data (1TB), could it be this?
>
>  There are no obvious messages in the logs though so I am a bit stumped
> as to why.I do not have the same trouble when impersonating other users
> with fairly full accounts. Perhaps a database issue (I do not know how to
> ‘cleanup’ the database or indeed Galaxy user accounts). Any thoughts?
>
>
>
> --
> Dr. Christian Schudoma
> Bioinformatics Support Officer
>
> Bioinformatics Group
> The Sainsbury Laboratory
> Norwich Research Park
> Norwich NR4 7UH
> United Kingdom
> **
> +44 (0) 1603 450 601
> christian.schud...@tsl.ac.uk
>
>  ___
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Re: [galaxy-dev] Switching history doesn't work with prefix

[Dannon Baker]

Great, glad it's working!

On Fri, Jul 24, 2015 at 6:00 AM Peter Cock 
wrote:

> Confirmed, updating to 15.05 fixed the switch history feature for us.
>
> http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html
>
> Now running:
>
> $ hg branch
> release_15.05
> $ hg log | head
> changeset:   17125:e837a68e8d14
> tag: tip
> parent:  17121:7a4e3a661a76
> parent:  17124:46a4ef8850b5
> user:Nate Coraor 
> date:Fri May 15 15:21:34 2015 -0400
> summary: Merge stable to default
>
> Thanks Dannon,
>
> Peter
>
> On Fri, Jul 24, 2015 at 10:41 AM, Peter Cock 
> wrote:
> > I think we were running 15.03.1,
> >
> > $ hg branch
> > stable
> > $ hg log | head
> > changeset:   17050:6395e7035143
> > tag: tip
> > parent:  17049:708cab19708d
> > parent:  17048:28113212
> > user:Nate Coraor 
> > date:Mon Mar 16 22:50:21 2015 -0400
> > summary: Merge v15.03.1 to default
> >
> > It sounds like updating to 15.05 should fix this then...
> >
> > Peter
> >
> > On Thu, Jul 23, 2015 at 8:57 PM, Ping Luo  wrote:
> >> Dannon,
> >>
> >> The release I am using is v15.03.
> >>
> >> Ping
> >>
> >> On Thu, Jul 23, 2015 at 10:15 AM, Dannon Baker 
> >> wrote:
> >>>
> >>> What revision are you running?  I'm seeing my proxy-prefix get appended
> >>> correctly in both release_15.05 and in current -dev.
> >>>
> >>> On Thu, Jul 23, 2015 at 5:10 AM Peter Cock 
> >>> wrote:
> >>>>
> >>>> Hello Ping,
> >>>>
> >>>> I can confirm this bug.
> >>>>
> >>>> I noticed this some time back when the new history was in beta,
> >>>> but neglected to explore what was wrong. Apologies.
> >>>>
> >>>> When looking at:
> >>>>
> >>>> http://our_server_name/galaxy/history/view_multiple
> >>>>
> >>>> Via Firefox I can see the "switch" button is triggering a URL like:
> >>>>
> >>>> http://our_server_name/history/set_as_current?id=cde77e676c9d11d1
> >>>>
> >>>> The Apache access log contains lines like this:
> >>>>
> >>>> "GET /history/set_as_current?id=cde77e676c9d11d1 HTTP/1.1" 404 294
> >>>> "http://our_server_name/galaxy/history/view_multiple"; "Mozilla/5.0
> >>>> (Macintosh; Intel Mac OS X 10.10; rv:39.0) Gecko/20100101
> >>>> Firefox/39.0"
> >>>>
> >>>> The Apache error log contains lines like this:
> >>>>
> >>>> File does not exist: /var/www/html/history, referer:
> >>>> http://our_server_name/galaxy/history/view_multiple
> >>>>
> >>>> We're using "galaxy" as a prefix for this instance using this in the
> >>>> config:
> >>>>
> >>>> [app:main]
> >>>> filter-with = proxy-prefix
> >>>> cookie_path = /galaxy
> >>>>
> >>>> Regards,
> >>>>
> >>>> Peter
> >>>>
> >>>> On Wed, Jul 22, 2015 at 8:26 PM, Ping Luo  wrote:
> >>>> > Hello,
> >>>> >
> >>>> > Our galaxy server is served under a sub-directory "/myserver". So
> far
> >>>> > everything works except the "Switch to" button in "view all
> history".
> >>>> > When
> >>>> > clicking it, there is no response. From apache server access log, I
> see
> >>>> > this
> >>>> > message
> >>>> >
> >>>> > "GET /history/set_as_current?id=9a8f74b3b768f8f1 HTTP/1.1" 404
> 304
> >>>> >
> >>>> > And in the apache error log, I see
> >>>> >
> >>>> >  File does not exist: /www/htdocs/history, referer:
> >>>> > https://xxx.xxx.xxx/myserver/history/view_multiple
> >>>> >
> >>>> > Since the prefix "/myserver" is not properly prepended in the
> equest,
> >>>> > the
> >>>> > request is not properly routed. It tries to retrive the history page
> >>>> > from
> >>>> > the document root /www/htdocs.
> >>>> >
> >>>> > So far, all other requests seems have a proper prefix, for example
> >>>> >
> >>>> > "GET /myserver/history/current_history_json HTTP/1.1" 200 1430
> >>>> > "GET /myserver/api/histories/7a11fc800eeb71e9/contents HTTP/1.1" 200
> >>>> > 15876
> >>>> > "GET /myserver/history/view_multiple HTTP/1.1" 200 27296
> >>>> > "GET /myserver/static/style/base.css?v=1437576796 HTTP/1.1" 304 -
> >>>> >
> >>>> >
> >>>> > Please help to resolve the issue.
> >>>> >
> >>>> > Thanks,
> >>>> >
> >>>> > Ping
> >>>> >
> >>>> >
>
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Re: [galaxy-dev] Switching history doesn't work with prefix

[Dannon Baker]

What revision are you running?  I'm seeing my proxy-prefix get appended
correctly in both release_15.05 and in current -dev.

On Thu, Jul 23, 2015 at 5:10 AM Peter Cock 
wrote:

> Hello Ping,
>
> I can confirm this bug.
>
> I noticed this some time back when the new history was in beta,
> but neglected to explore what was wrong. Apologies.
>
> When looking at:
>
> http://our_server_name/galaxy/history/view_multiple
>
> Via Firefox I can see the "switch" button is triggering a URL like:
>
> http://our_server_name/history/set_as_current?id=cde77e676c9d11d1
>
> The Apache access log contains lines like this:
>
> "GET /history/set_as_current?id=cde77e676c9d11d1 HTTP/1.1" 404 294
> "http://our_server_name/galaxy/history/view_multiple"; "Mozilla/5.0
> (Macintosh; Intel Mac OS X 10.10; rv:39.0) Gecko/20100101
> Firefox/39.0"
>
> The Apache error log contains lines like this:
>
> File does not exist: /var/www/html/history, referer:
> http://our_server_name/galaxy/history/view_multiple
>
> We're using "galaxy" as a prefix for this instance using this in the
> config:
>
> [app:main]
> filter-with = proxy-prefix
> cookie_path = /galaxy
>
> Regards,
>
> Peter
>
> On Wed, Jul 22, 2015 at 8:26 PM, Ping Luo  wrote:
> > Hello,
> >
> > Our galaxy server is served under a sub-directory "/myserver". So far
> > everything works except the "Switch to" button in "view all history".
> When
> > clicking it, there is no response. From apache server access log, I see
> this
> > message
> >
> > "GET /history/set_as_current?id=9a8f74b3b768f8f1 HTTP/1.1" 404 304
> >
> > And in the apache error log, I see
> >
> >  File does not exist: /www/htdocs/history, referer:
> > https://xxx.xxx.xxx/myserver/history/view_multiple
> >
> > Since the prefix "/myserver" is not properly prepended in the equest, the
> > request is not properly routed. It tries to retrive the history page from
> > the document root /www/htdocs.
> >
> > So far, all other requests seems have a proper prefix, for example
> >
> > "GET /myserver/history/current_history_json HTTP/1.1" 200 1430
> > "GET /myserver/api/histories/7a11fc800eeb71e9/contents HTTP/1.1" 200
> 15876
> > "GET /myserver/history/view_multiple HTTP/1.1" 200 27296
> > "GET /myserver/static/style/base.css?v=1437576796 HTTP/1.1" 304 -
> >
> >
> > Please help to resolve the issue.
> >
> > Thanks,
> >
> > Ping
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
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Re: [galaxy-dev] Galaxy admin access

[Dannon Baker]

Did you restart the server after editing galaxy.ini?  That, and refreshing
the main page should be all you need to do, and you'll see a new "Admin"
menu in the top masthead when logged in as the admin user.

And, just to confirm -- you have registered a user with the corresponding
email address on this Galaxy instance, correct?

On Tue, Jun 23, 2015 at 8:26 AM Davenport, Aneisha  wrote:

>  I followed the instructions however I still cannot tell if I have been
> given administration access. The galaxy screen at http://localhost:8080
> looks the same
>
>
>  Original message 
> From: Dannon Baker 
> Date: 06/23/2015 8:20 AM (GMT-05:00)
> To: "Davenport, Aneisha" ,
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Galaxy admin access
>
>  Sure, you can change those if you'd like for it to run on a different
> port, etc -- otherwise these settings will use default values (the same
> ones you've been using already).  The only setting you'll have to change to
> get admin access is admin_users.
>
>  On Tue, Jun 23, 2015 at 8:15 AM Davenport, Aneisha 
> wrote:
>
>>  Do I have to change host, port or username info and remove (#)
>>
>>
>>  Original message 
>> From: Dannon Baker 
>>  Date: 06/23/2015 7:38 AM (GMT-05:00)
>> To: "Davenport, Aneisha" ,
>> galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Galaxy admin access
>>
>>  Ok, that should work fine.  Are you now able to edit that galaxy.ini in
>> text wrangler?  If so, find the admin_users line and add your email address
>> and any others to the line and uncomment it -- make sure it doesn't start
>> with a # anymore.
>>
>>  So, it'll be:
>> admin_users = adave...@gru.edu, us...@gmail.com
>>
>>  On Tue, Jun 23, 2015 at 7:25 AM Davenport, Aneisha 
>> wrote:
>>
>>>  I created galaxy.ini using (text wrangler)by copying the contents in
>>> galaxy .ini.sample and putting galaxy.ini in that same folder.
>>> (Galaxy/config) Should I delete that file? If so what are the exact steps
>>> and commands should I place in terminal for administrative access?
>>>
>>>
>>>  Original message 
>>> From: Dannon Baker 
>>>  Date: 06/17/2015 12:21 PM (GMT-05:00)
>>> To: "Davenport, Aneisha" ,
>>> galaxy-dev@lists.galaxyproject.org
>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>
>>>  In your terminal, you'll need to navigate to the galaxy config
>>> directory (you'll see the .sample file there) first.  Once there, look at a
>>> directory list and make sure that an existing galaxy.ini isn't already
>>> there.
>>>
>>> Also, please keep the galaxy-dev list cc'd instead of replying directly
>>> so that others might be able to help you as well.
>>>
>>>
>>>  On Wed, Jun 17, 2015 at 12:18 PM Davenport, Aneisha 
>>> wrote:
>>>
>>>>  I'm typing the command in terminal
>>>>
>>>>
>>>>  Original message 
>>>> From: Dannon Baker 
>>>>  Date: 06/17/2015 12:05 PM (GMT-05:00)
>>>> To: "Davenport, Aneisha" ,
>>>> galaxy-dev@lists.galaxyproject.org
>>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>>
>>>>  Where are you executing this?  You'll need to be in the galaxy/config
>>>> directory, where galaxy.ini.sample exists.
>>>>
>>>> I'm looping the mailing list back in on this so other people might also
>>>> be able to help.
>>>>
>>>>  On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha 
>>>> wrote:
>>>>
>>>>> When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs
>>>>> no such file or directory
>>>>>
>>>>>
>>>>>  Original message 
>>>>> From: Dannon Baker 
>>>>> Date: 06/15/2015 3:14 PM (GMT-05:00)
>>>>> To: "Davenport, Aneisha" 
>>>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>>>
>>>>>  I'm not sure what you mean.  You can edit the file using any text
>>>>> editor, try 'nano', or emacs or vim if you're more comfortable with those.
>>>>>
>>>>>  Does the file exist or not?  If not, simply "cp galaxy.ini.sample
>>>>> galaxy.ini" will do it.
>>>>>
&g

Re: [galaxy-dev] Galaxy admin access

[Dannon Baker]

Sure, you can change those if you'd like for it to run on a different port,
etc -- otherwise these settings will use default values (the same ones
you've been using already).  The only setting you'll have to change to get
admin access is admin_users.

On Tue, Jun 23, 2015 at 8:15 AM Davenport, Aneisha  wrote:

>  Do I have to change host, port or username info and remove (#)
>
>
>  Original message ----
> From: Dannon Baker 
> Date: 06/23/2015 7:38 AM (GMT-05:00)
> To: "Davenport, Aneisha" ,
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Galaxy admin access
>
>  Ok, that should work fine.  Are you now able to edit that galaxy.ini in
> text wrangler?  If so, find the admin_users line and add your email address
> and any others to the line and uncomment it -- make sure it doesn't start
> with a # anymore.
>
>  So, it'll be:
> admin_users = adave...@gru.edu, us...@gmail.com
>
>  On Tue, Jun 23, 2015 at 7:25 AM Davenport, Aneisha 
> wrote:
>
>>  I created galaxy.ini using (text wrangler)by copying the contents in
>> galaxy .ini.sample and putting galaxy.ini in that same folder.
>> (Galaxy/config) Should I delete that file? If so what are the exact steps
>> and commands should I place in terminal for administrative access?
>>
>>
>>  Original message 
>> From: Dannon Baker 
>>  Date: 06/17/2015 12:21 PM (GMT-05:00)
>> To: "Davenport, Aneisha" ,
>> galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Galaxy admin access
>>
>>  In your terminal, you'll need to navigate to the galaxy config
>> directory (you'll see the .sample file there) first.  Once there, look at a
>> directory list and make sure that an existing galaxy.ini isn't already
>> there.
>>
>> Also, please keep the galaxy-dev list cc'd instead of replying directly
>> so that others might be able to help you as well.
>>
>>
>>  On Wed, Jun 17, 2015 at 12:18 PM Davenport, Aneisha 
>> wrote:
>>
>>>  I'm typing the command in terminal
>>>
>>>
>>>  Original message 
>>> From: Dannon Baker 
>>>  Date: 06/17/2015 12:05 PM (GMT-05:00)
>>> To: "Davenport, Aneisha" ,
>>> galaxy-dev@lists.galaxyproject.org
>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>
>>>  Where are you executing this?  You'll need to be in the galaxy/config
>>> directory, where galaxy.ini.sample exists.
>>>
>>> I'm looping the mailing list back in on this so other people might also
>>> be able to help.
>>>
>>>  On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha 
>>> wrote:
>>>
>>>> When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs
>>>> no such file or directory
>>>>
>>>>
>>>>  Original message 
>>>> From: Dannon Baker 
>>>> Date: 06/15/2015 3:14 PM (GMT-05:00)
>>>> To: "Davenport, Aneisha" 
>>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>>
>>>>  I'm not sure what you mean.  You can edit the file using any text
>>>> editor, try 'nano', or emacs or vim if you're more comfortable with those.
>>>>
>>>>  Does the file exist or not?  If not, simply "cp galaxy.ini.sample
>>>> galaxy.ini" will do it.
>>>>
>>>>  On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha 
>>>> wrote:
>>>>
>>>>> How do I create it and edit it on terminal?
>>>>>
>>>>> Aneisha Davenport
>>>>> 
>>>>> From: Dannon Baker [dannon.ba...@gmail.com]
>>>>> Sent: Friday, June 12, 2015 9:44 PM
>>>>> To: Davenport, Aneisha; galaxy-dev@lists.galaxyproject.org
>>>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>>>
>>>>> Hi Aneisha,
>>>>>
>>>>> When you say you cannot alter config/galaxy.ini, what do you mean?
>>>>> You should be able to create (if not there) and edit this file in your
>>>>> regular terminal on that machine.
>>>>>
>>>>> Does a different user own the file, perhaps a 'galaxy' one?  If so,
>>>>> you could change to that user and then edit.
>>>>>
>>>>> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha >>>> <mailto:adave...@gru.e

Re: [galaxy-dev] Galaxy admin access

[Dannon Baker]

Ok, that should work fine.  Are you now able to edit that galaxy.ini in
text wrangler?  If so, find the admin_users line and add your email address
and any others to the line and uncomment it -- make sure it doesn't start
with a # anymore.

So, it'll be:
admin_users = adave...@gru.edu, us...@gmail.com

On Tue, Jun 23, 2015 at 7:25 AM Davenport, Aneisha  wrote:

>  I created galaxy.ini using (text wrangler)by copying the contents in
> galaxy .ini.sample and putting galaxy.ini in that same folder.
> (Galaxy/config) Should I delete that file? If so what are the exact steps
> and commands should I place in terminal for administrative access?
>
>
>  Original message 
> From: Dannon Baker 
> Date: 06/17/2015 12:21 PM (GMT-05:00)
> To: "Davenport, Aneisha" ,
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Galaxy admin access
>
>  In your terminal, you'll need to navigate to the galaxy config directory
> (you'll see the .sample file there) first.  Once there, look at a directory
> list and make sure that an existing galaxy.ini isn't already there.
>
> Also, please keep the galaxy-dev list cc'd instead of replying directly so
> that others might be able to help you as well.
>
>
>  On Wed, Jun 17, 2015 at 12:18 PM Davenport, Aneisha 
> wrote:
>
>>  I'm typing the command in terminal
>>
>>
>>  Original message 
>> From: Dannon Baker 
>>  Date: 06/17/2015 12:05 PM (GMT-05:00)
>> To: "Davenport, Aneisha" ,
>> galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Galaxy admin access
>>
>>  Where are you executing this?  You'll need to be in the galaxy/config
>> directory, where galaxy.ini.sample exists.
>>
>> I'm looping the mailing list back in on this so other people might also
>> be able to help.
>>
>>  On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha 
>> wrote:
>>
>>> When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs no
>>> such file or directory
>>>
>>>
>>>  Original message 
>>> From: Dannon Baker 
>>> Date: 06/15/2015 3:14 PM (GMT-05:00)
>>> To: "Davenport, Aneisha" 
>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>
>>>  I'm not sure what you mean.  You can edit the file using any text
>>> editor, try 'nano', or emacs or vim if you're more comfortable with those.
>>>
>>>  Does the file exist or not?  If not, simply "cp galaxy.ini.sample
>>> galaxy.ini" will do it.
>>>
>>>  On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha 
>>> wrote:
>>>
>>>> How do I create it and edit it on terminal?
>>>>
>>>> Aneisha Davenport
>>>> 
>>>> From: Dannon Baker [dannon.ba...@gmail.com]
>>>> Sent: Friday, June 12, 2015 9:44 PM
>>>> To: Davenport, Aneisha; galaxy-dev@lists.galaxyproject.org
>>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>>
>>>> Hi Aneisha,
>>>>
>>>> When you say you cannot alter config/galaxy.ini, what do you mean?  You
>>>> should be able to create (if not there) and edit this file in your regular
>>>> terminal on that machine.
>>>>
>>>> Does a different user own the file, perhaps a 'galaxy' one?  If so, you
>>>> could change to that user and then edit.
>>>>
>>>> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha >>> <mailto:adave...@gru.edu>> wrote:
>>>> Hi, I work at the It service desk at the GRU Health and Science campus
>>>> Ed Commons GB building and I have a customer trying to get admin access for
>>>> the local installation of galaxy. We tried to follow the online
>>>> instructions "In order to control your new Galaxy through the UI
>>>> (installing tools, managing users, creating groups etc.) you have to become
>>>> an administrator. First register as a new user and then give the user admin
>>>> privileges like this: You add the Galaxy login ( email ) to the Galaxy
>>>> configuration file (config/galaxy.ini). If the file does not exist you can
>>>> copy it from the provided sample (config/galaxy.ini.sample). Note that you
>>>> have to restart Galaxy after modifying the configuration for changes to
>>>> take effect.
>>>>
>>>>
>>>> # this should be a comma-separated list of valid 

Re: [galaxy-dev] Galaxy admin access

[Dannon Baker]

In your terminal, you'll need to navigate to the galaxy config directory
(you'll see the .sample file there) first.  Once there, look at a directory
list and make sure that an existing galaxy.ini isn't already there.

Also, please keep the galaxy-dev list cc'd instead of replying directly so
that others might be able to help you as well.


On Wed, Jun 17, 2015 at 12:18 PM Davenport, Aneisha 
wrote:

>  I'm typing the command in terminal
>
>
> ---- Original message 
> From: Dannon Baker 
> Date: 06/17/2015 12:05 PM (GMT-05:00)
> To: "Davenport, Aneisha" ,
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Galaxy admin access
>
>  Where are you executing this?  You'll need to be in the galaxy/config
> directory, where galaxy.ini.sample exists.
>
> I'm looping the mailing list back in on this so other people might also be
> able to help.
>
>  On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha 
> wrote:
>
>> When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs no
>> such file or directory
>>
>>
>>  Original message 
>> From: Dannon Baker 
>> Date: 06/15/2015 3:14 PM (GMT-05:00)
>> To: "Davenport, Aneisha" 
>> Subject: Re: [galaxy-dev] Galaxy admin access
>>
>>  I'm not sure what you mean.  You can edit the file using any text
>> editor, try 'nano', or emacs or vim if you're more comfortable with those.
>>
>>  Does the file exist or not?  If not, simply "cp galaxy.ini.sample
>> galaxy.ini" will do it.
>>
>>  On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha 
>> wrote:
>>
>>> How do I create it and edit it on terminal?
>>>
>>> Aneisha Davenport
>>> 
>>> From: Dannon Baker [dannon.ba...@gmail.com]
>>> Sent: Friday, June 12, 2015 9:44 PM
>>> To: Davenport, Aneisha; galaxy-dev@lists.galaxyproject.org
>>> Subject: Re: [galaxy-dev] Galaxy admin access
>>>
>>> Hi Aneisha,
>>>
>>> When you say you cannot alter config/galaxy.ini, what do you mean?  You
>>> should be able to create (if not there) and edit this file in your regular
>>> terminal on that machine.
>>>
>>> Does a different user own the file, perhaps a 'galaxy' one?  If so, you
>>> could change to that user and then edit.
>>>
>>> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha >> <mailto:adave...@gru.edu>> wrote:
>>> Hi, I work at the It service desk at the GRU Health and Science campus
>>> Ed Commons GB building and I have a customer trying to get admin access for
>>> the local installation of galaxy. We tried to follow the online
>>> instructions "In order to control your new Galaxy through the UI
>>> (installing tools, managing users, creating groups etc.) you have to become
>>> an administrator. First register as a new user and then give the user admin
>>> privileges like this: You add the Galaxy login ( email ) to the Galaxy
>>> configuration file (config/galaxy.ini). If the file does not exist you can
>>> copy it from the provided sample (config/galaxy.ini.sample). Note that you
>>> have to restart Galaxy after modifying the configuration for changes to
>>> take effect.
>>>
>>>
>>> # this should be a comma-separated list of valid Galaxy users
>>> admin_users = us...@example.com<mailto:us...@example.com>,
>>> us...@example.com<mailto:us...@example.com>" but we cannot alter the
>>> config/galaxy.ini file. Can you please give us assistance? Do you run in
>>> console or Terminal (this is a Macbook Air Laptop)?
>>>
>>>
>>> Aneisha Davenport
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] functional tests / database lock

[Dannon Baker]

Thanks, I'll take a look.  Non-tool-based functional tests should *not*
fail out of the box, and we'll fix them :)

On Wed, Jun 17, 2015 at 12:04 PM Ryan G  wrote:

> All the functional.test_admin_features
> Most of the functional.test_data_security
> functional.test_history_functions
>
> I'm attaching a PDF printout of the run_functional_tests.html
>
>
>
> On Wed, Jun 17, 2015 at 12:01 PM, Dannon Baker 
> wrote:
>
>> Which tests are failing, specifically?  Many tests will fail without the
>> underlying tools installed.
>>
>> On Wed, Jun 17, 2015 at 12:01 PM Ryan G 
>> wrote:
>>
>>> I've migrated my staging instance to use postgres and ran the functional
>>> tests.  I see lots failing.  I know this is known and perhaps expected, but
>>> it still bothers me.  I would expect to see all the tests pass on a clean
>>> instance.  If the tests aren't passing, to me, that indicates a problem
>>> somewhere.  What's the point in having the tests if they always fail?
>>>
>>>
>>>
>>> On Tue, Jun 16, 2015 at 1:12 PM, Ryan G 
>>> wrote:
>>>
>>>> I am using postgres in production but want to validate my staging
>>>> instance before pushing it into production.  I do this with the functional
>>>> tests.  I guess I'll have to set up a postgres database for the staging
>>>> instance as well.
>>>>
>>>>
>>>> On Mon, Jun 15, 2015 at 10:32 AM, John Chilton 
>>>> wrote:
>>>>
>>>>> Not exactly - I feel like sqlite should be able to do the kinds of
>>>>> things Galaxy does without this occurring - it should just be
>>>>> inefficient. We are probably doing something across multiple threads
>>>>> that we should not be - presumably related to job handling. After a
>>>>> recent sqlalchemy upgrade - there is now a new error message in the
>>>>> logs that should help track down the problem:
>>>>>
>>>>> sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception
>>>>> during reset or similar
>>>>> Traceback (most recent call last):
>>>>>   File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in
>>>>> _finalize_fairy
>>>>> fairy._reset(pool)
>>>>>   File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in
>>>>> _reset
>>>>> pool._dialect.do_rollback(self)
>>>>>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py",
>>>>> line 412, in do_rollback
>>>>> dbapi_connection.rollback()
>>>>> ProgrammingError: SQLite objects created in a thread can only be used
>>>>> in that same thread.The object was created in thread id
>>>>> 140442561648384 and this is thread id 140442989479680
>>>>>
>>>>> At any rate - we recommend using postgres in production for a reason -
>>>>> these sqlite errors are pretty common.
>>>>>
>>>>> -John
>>>>>
>>>>>
>>>>> On Fri, Jun 12, 2015 at 11:15 AM, Ryan G 
>>>>> wrote:
>>>>> > Is there a known cause for this?
>>>>> >
>>>>> > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo <
>>>>> nsora...@tiscali.it>
>>>>> > wrote:
>>>>> >>
>>>>> >> Hi Ryan,
>>>>> >> there is no know fix for this, apart from moving to PostgreSQL.
>>>>> >>
>>>>> >> Cheers,
>>>>> >> Nicola
>>>>> >>
>>>>> >> Il 12.06.2015 16:43 Ryan G ha scritto:
>>>>> >>
>>>>> >> Hi all - I'm running functional tests on a set of tools using
>>>>> >> 'run_tests.sh -sid ...'.  A few of the tests fail.  When I go back
>>>>> and run
>>>>> >> the tool tests individually, they succeed.  So I looked into why
>>>>> they fail
>>>>> >> when running them in batch, and it turns out to be a database
>>>>> lock.  I'm
>>>>> >> using the default sqllite database that run_tests.sh creates.  Does
>>>>> this
>>>>> >> need to be tuned somehow?
>>>>> >>
>>>>> >>
>>>>> >> galaxy.jobs.handler INFO 2015-06-1

Re: [galaxy-dev] Galaxy admin access

[Dannon Baker]

Where are you executing this?  You'll need to be in the galaxy/config
directory, where galaxy.ini.sample exists.

I'm looping the mailing list back in on this so other people might also be
able to help.

On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha  wrote:

>  When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs no
> such file or directory
>
>
>  Original message 
> From: Dannon Baker 
> Date: 06/15/2015 3:14 PM (GMT-05:00)
> To: "Davenport, Aneisha" 
> Subject: Re: [galaxy-dev] Galaxy admin access
>
>  I'm not sure what you mean.  You can edit the file using any text
> editor, try 'nano', or emacs or vim if you're more comfortable with those.
>
>  Does the file exist or not?  If not, simply "cp galaxy.ini.sample
> galaxy.ini" will do it.
>
>  On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha 
> wrote:
>
>> How do I create it and edit it on terminal?
>>
>> Aneisha Davenport
>> 
>> From: Dannon Baker [dannon.ba...@gmail.com]
>> Sent: Friday, June 12, 2015 9:44 PM
>> To: Davenport, Aneisha; galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Galaxy admin access
>>
>> Hi Aneisha,
>>
>> When you say you cannot alter config/galaxy.ini, what do you mean?  You
>> should be able to create (if not there) and edit this file in your regular
>> terminal on that machine.
>>
>> Does a different user own the file, perhaps a 'galaxy' one?  If so, you
>> could change to that user and then edit.
>>
>> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha > <mailto:adave...@gru.edu>> wrote:
>> Hi, I work at the It service desk at the GRU Health and Science campus Ed
>> Commons GB building and I have a customer trying to get admin access for
>> the local installation of galaxy. We tried to follow the online
>> instructions "In order to control your new Galaxy through the UI
>> (installing tools, managing users, creating groups etc.) you have to become
>> an administrator. First register as a new user and then give the user admin
>> privileges like this: You add the Galaxy login ( email ) to the Galaxy
>> configuration file (config/galaxy.ini). If the file does not exist you can
>> copy it from the provided sample (config/galaxy.ini.sample). Note that you
>> have to restart Galaxy after modifying the configuration for changes to
>> take effect.
>>
>>
>> # this should be a comma-separated list of valid Galaxy users
>> admin_users = us...@example.com<mailto:us...@example.com>,
>> us...@example.com<mailto:us...@example.com>" but we cannot alter the
>> config/galaxy.ini file. Can you please give us assistance? Do you run in
>> console or Terminal (this is a Macbook Air Laptop)?
>>
>>
>> Aneisha Davenport
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] functional tests / database lock

[Dannon Baker]

Which tests are failing, specifically?  Many tests will fail without the
underlying tools installed.

On Wed, Jun 17, 2015 at 12:01 PM Ryan G  wrote:

> I've migrated my staging instance to use postgres and ran the functional
> tests.  I see lots failing.  I know this is known and perhaps expected, but
> it still bothers me.  I would expect to see all the tests pass on a clean
> instance.  If the tests aren't passing, to me, that indicates a problem
> somewhere.  What's the point in having the tests if they always fail?
>
>
>
> On Tue, Jun 16, 2015 at 1:12 PM, Ryan G 
> wrote:
>
>> I am using postgres in production but want to validate my staging
>> instance before pushing it into production.  I do this with the functional
>> tests.  I guess I'll have to set up a postgres database for the staging
>> instance as well.
>>
>>
>> On Mon, Jun 15, 2015 at 10:32 AM, John Chilton 
>> wrote:
>>
>>> Not exactly - I feel like sqlite should be able to do the kinds of
>>> things Galaxy does without this occurring - it should just be
>>> inefficient. We are probably doing something across multiple threads
>>> that we should not be - presumably related to job handling. After a
>>> recent sqlalchemy upgrade - there is now a new error message in the
>>> logs that should help track down the problem:
>>>
>>> sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception
>>> during reset or similar
>>> Traceback (most recent call last):
>>>   File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in
>>> _finalize_fairy
>>> fairy._reset(pool)
>>>   File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in
>>> _reset
>>> pool._dialect.do_rollback(self)
>>>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py",
>>> line 412, in do_rollback
>>> dbapi_connection.rollback()
>>> ProgrammingError: SQLite objects created in a thread can only be used
>>> in that same thread.The object was created in thread id
>>> 140442561648384 and this is thread id 140442989479680
>>>
>>> At any rate - we recommend using postgres in production for a reason -
>>> these sqlite errors are pretty common.
>>>
>>> -John
>>>
>>>
>>> On Fri, Jun 12, 2015 at 11:15 AM, Ryan G 
>>> wrote:
>>> > Is there a known cause for this?
>>> >
>>> > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo 
>>> > wrote:
>>> >>
>>> >> Hi Ryan,
>>> >> there is no know fix for this, apart from moving to PostgreSQL.
>>> >>
>>> >> Cheers,
>>> >> Nicola
>>> >>
>>> >> Il 12.06.2015 16:43 Ryan G ha scritto:
>>> >>
>>> >> Hi all - I'm running functional tests on a set of tools using
>>> >> 'run_tests.sh -sid ...'.  A few of the tests fail.  When I go back
>>> and run
>>> >> the tool tests individually, they succeed.  So I looked into why they
>>> fail
>>> >> when running them in batch, and it turns out to be a database lock.
>>> I'm
>>> >> using the default sqllite database that run_tests.sh creates.  Does
>>> this
>>> >> need to be tuned somehow?
>>> >>
>>> >>
>>> >> galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched
>>> >> Error - : (OperationalError) database is locked u'SELECT api_keys.id
>>> AS
>>> >> api_keys_id, api_keys.create_time AS api_keys_create_time,
>>> api_keys.user_id
>>> >> AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys
>>> \nWHERE
>>> >> api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
>>> >> URL:
>>> >>
>>> http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
>>> >> line 149 in __call__
>>> >>   app_iter = self.application(environ, sr_checker)
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>>> >> line 84 in __call__
>>> >>   return self.application(environ, start_response)
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>>> >> line 633 in __call__
>>> >>   return self.application(environ, start_response)
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
>>> >> line 132 in __call__
>>> >>   return self.handle_request( environ, start_response )
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
>>> >> line 159 in handle_request
>>> >>   trans = self.transaction_factory( environ )
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
>>> >> line 71 in
>>> >>   self.set_transaction_factory( lambda e: self.transaction_chooser( e,
>>> >> galaxy_app, session_cookie ) )
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
>>> >> line 102 in transaction_chooser
>>> >>   return GalaxyWebTransaction( environ, galaxy_app, self,
>>> session_cookie )
>>> >> File
>>> >>
>>> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/we

Re: [galaxy-dev] Bug in galaxy-dist/latest_15.05 for "Share history with user" function

[Dannon Baker]

Hey Peter, this was indeed reported and fixed in
https://github.com/galaxyproject/galaxy/commit/7294bd0af33bc974684c8ed8d21e97017660ca22,
which should already be available in the release_15.05 branch of the
repository if you update.

Sorry for the trouble, and even though it's resolved now, thanks for taking
the time to debug this and write such a detailed error report including a
patch!


-Dannon

On Wed, Jun 17, 2015 at 9:03 AM Peter Briggs 
wrote:

> Hello
>
> I think a bug was introduced into galaxy-dist between the 15.03 and
> 15.05 releases, for the "Share history with user" function. The function
> works for 15.03 but fails in 15.05.
>
> To reproduce:
> 1. Click on the "cog" icon for a history and select "Share or publish"
> 2. Under "Share History with Individual Users" click "Share with a user"
> 3. Enter the email of another user on the system and click submit
>
> In 15.03 this returns to the sharing screen and indicates that the
> history has been shared with the specified user; in 15.05 this produces
> a stack trace (or "internal server error" in a production setting").
>
> The following patch appears to fix the problem:
>
> diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py
> --- a/lib/galaxy/webapps/galaxy/controllers/history.py  Fri May 15
> 15:20:17 2015 -0400
> +++ b/lib/galaxy/webapps/galaxy/controllers/history.py  Wed Jun 17
> 12:51:41 2015 +0100
> @@ -899,7 +899,7 @@
>   for history_id in ids:
>   history_id = self.decode_id( history_id )
>   history = self.history_manager.get_owned( history_id,
> trans.user, current_history=trans.history )
> -histories.append(  )
> +histories.append( history )
>   return histories
>
>   def _get_users( self, trans, user, emails_or_ids ):
>
> also available via this gist:
>
> https://gist.github.com/pjbriggs/65c29a87e094d4d257f6
>
> Apologies if this has already been reported/fixed elsewhere, or if
> there's a better way to submit this fix (if so then please let me know)
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Galaxy admin access

[Dannon Baker]

Hi Aneisha,

When you say you cannot alter config/galaxy.ini, what do you mean?  You
should be able to create (if not there) and edit this file in your regular
terminal on that machine.

Does a different user own the file, perhaps a 'galaxy' one?  If so, you
could change to that user and then edit.

On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha  wrote:

> Hi, I work at the It service desk at the GRU Health and Science campus Ed
> Commons GB building and I have a customer trying to get admin access for
> the local installation of galaxy. We tried to follow the online
> instructions "In order to control your new Galaxy through the UI
> (installing tools, managing users, creating groups etc.) you have to become
> an administrator. First register as a new user and then give the user admin
> privileges like this: You add the Galaxy login ( email ) to the Galaxy
> configuration file (config/galaxy.ini). If the file does not exist you can
> copy it from the provided sample (config/galaxy.ini.sample). Note that you
> have to restart Galaxy after modifying the configuration for changes to
> take effect.
>
>
> # this should be a comma-separated list of valid Galaxy users
> admin_users = us...@example.com,us...@example.com" but we cannot alter
> the config/galaxy.ini file. Can you please give us assistance? Do you run
> in console or Terminal (this is a Macbook Air Laptop)?
>
>
> Aneisha Davenport
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Re: [galaxy-dev] galaxy upgrade

[Dannon Baker]

Hi Don,

Yes, with each release we now have official release notes that contain
information on how to update, in addition to detailing the changes you
should expect to see.  If you have an older instance, your repository is
probably mercurial based, so it should be a simple 'hg pull' 'hg update
latest_15.05' to update to the current 15.05 release.  Here's a link to the
full release doc with more information:

http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html

-Dannon

On Thu, May 28, 2015 at 8:30 AM Shrum, Donald C 
wrote:

>  Is there an official upgrade process for galaxy?  I’d like to upgrade to
> the latest version with ldap support.   We have a small user base here at
> FSU but I’d like to avoid just wiping out the existing tools.
>
>
>
> --Don
>
> Florida State University
>
> Research Computing Center
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Re: [galaxy-dev] missing auth_conf.xml.sample

[Dannon Baker]

Thanks for catching this, we'll be updating the bitbucket release shortly
to correctly include the new .sample.

On Fri, May 15, 2015 at 2:05 PM Will Holtz  wrote:

> Here is the file:
>
> https://raw.githubusercontent.com/galaxyproject/galaxy/dev/config/auth_conf.xml.sample
>
> -Will
>
>
> On Fri, May 15, 2015 at 10:59 AM, Tony Kusalik 
> wrote:
>
>> Hi
>>
>> This morning I did a hg pull -u
>> This took me from
>>   changeset:   17103
>> to
>>   changeset:   17121:7a4e3a661a76
>>
>> However, when trying to restart the galaxy server, I get
>>   IOError: [Errno 2] No such file or directory:
>> './config/auth_conf.xml.sample'
>>
>> Checking the config subdirectory, I can confirm that this .xml.sample
>> file is not
>> present.
>>
>> Where can I get a copy of config/auth_conf.xml.sample?
>>   (I'd rather just grab this file rather than doing something as drastic
>> as a re-install.)
>> Why did the update not pull down a copy of  config/auth_conf.xml.sample?
>> Did I do
>> something wrong?
>>
>> Thanks.
>>
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>
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