Re: [galaxy-dev] Get the user credentials from the tool.

[John Chilton]

Hello Dmitry,

This use case isn't really addressed by Galaxy currently.

There is not a generic way of doing grabbing the users credentials
like this or producing URLs from inside the tool. This depends on a
lot of different things - how Galaxy's proxy is configured, etc... so
in many (all?) cases Galaxy would not be able to fetch the users raw
credentials. Your best bet is going to be to use the Galaxy's API -
tools can fetch a user's API key and you can use Galaxy's API to build
a URL that includes this key.

Your users will all need API keys set to use the tool. There have been
some other galaxy-dev discussions about using the API from tools -
http://osdir.com/ml/galaxy-development-source-control/2013-12/msg00105.html.
In general I would discourage this because it is difficult to do in a
generic way - for instance there is no way for the tool to accurately
determine what the URL of Galaxy should be - but it should be possible
to tailor something to your setup if absolutely needed.

If you are really keen to use the Galaxy API to do this and you
understand the limitations - we can try to work through the exact
details.

If it is at all possible to send the data to the web service instead
of sending a reference - the genomespace exporter
(https://bitbucket.org/galaxy/galaxy-central/src/74b6e23ed7882f3c091d2b66ce85025241372017/tools/genomespace/genomespace_exporter.xml?at=default)
might be a good example of how to do this in a more generic fashion.

-John


On Tue, Apr 29, 2014 at 11:16 AM, Dmitry  wrote:
> Hello,
>
> Is there any way to provide a protected resource link to the external
> application?
> My tool is supposed to call a Web service via SSL which should access to the
> Galaxy resources.
> In ideal it would be something like
> ftp://user:passw...@mygalaxy.net/fasta.gz
>
> The Web service then downloads the resource and do the computation.
>
> Since user is already provided the login to galaxy, I do not want to ask the
> password again on a tool page.
>
> Sincerely,
>
> Dmitry
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[galaxy-dev] Uploading big data in local installation of galaxy

[Jennifer Jackson]

Hi Amit,

You may have solved this already, but if not, there are (at least) two 
good options, with the second better if your data is already on the same 
computer that you have Galaxy running. A file 2G or over will never load 
through the browser - this same rule applies to a local and the public 
Main site (and anywhere else that I am aware of).


Start by setting with a basic 'production' configuration
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

1 - Enable FTP as described in the link above

2 - Load the data into a library through one of these options
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

I am going to post this to the galaxy-dev list to help others that may 
have the same question. Next time, for the speediest reply, post 
directly here with local admin questions. You'll benefit from replies 
from our team and the community (super helpful!).


Best,

Jen
Galaxy team


Dear Jennifer,

I installed galaxy locally on my linux machine including the tool 
shed, but the file upload keeps
showing the "uploading" status forever for big datasets ( for example 
CAGE reads > 6GB).


Could you please help in sorting out the problem ?

warm regards,
Amit.


--
Jennifer Hillman-Jackson
http://galaxyproject.org

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Re: [galaxy-dev] permanently deleting histories

[Jennifer Jackson]

Hi Jennifer,

Active and Deleted histories can be permanently deleted using from the 
History pane "Options -> Saved Histories", then at the top of the middle 
panel click on "Advanced Search", then click on "status: all". Check the 
box for the histories to be discarded and then click on the button 
"Permanently delete".


Full instructions with a video walk-through are here:
https://wiki.galaxyproject.org/Learn/ManagingDatasets#Delete_vs_Delete_Permanently

Best,

Jen
Galaxy team

On 5/5/14 10:33 AM, Jennifer Gotenstein wrote:
I need to clear space from my quota of usage in my galaxy main user 
account, but I deleted 2 histories, rather than permanently deleting 
them. How can I access them again so that I may permanently delete 
them to clear the space?


Thank you,

Jennifer


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--
Jennifer Hillman-Jackson
http://galaxyproject.org

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[galaxy-dev] permanently deleting histories

[Jennifer Gotenstein]

I need to clear space from my quota of usage in my galaxy main user
account, but I deleted 2 histories, rather than permanently deleting them.
How can I access them again so that I may permanently delete them to clear
the space?

Thank you,

Jennifer
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Re: [galaxy-dev] Portability and versionig in Galaxy

[Jennifer Jackson]

Hi Sally,

I can point you to a few resources that explain what we are working on, 
what we plan to work on, and how the architecture is put together. All 
possible development directions versus what is prioritized because it 
fits the larger project goals will be hopefully be clearer after a 
review. Galaxy development is highly collaborative and we do our best to 
be transparent. Anyone can freely publish work within our framework to 
share with others also using Galaxy (tools in the Tool Shed, 
data/analysis/workflows/etc. on the public server).


Looks for changes across time for workflows in releases here:
https://wiki.galaxyproject.org/DevNewsBriefs

Read our publications about architecture here:
https://wiki.galaxyproject.org/CitingGalaxy

Trello cards for ideas, in-progress, recently completed work (all areas):
https://wiki.galaxyproject.org/Issues

Code documentation:
http://galaxy-dist.readthedocs.org/en/latest/

Take care,

Jen
Galaxy team

On 4/30/14 2:29 PM, Golestan (Sally) Radwan wrote:

Hi All,

I am completely new to galaxy but part of my PhD research is to look 
at portability issues of workloads across different versions. I've 
tried looking at the wiki and the various pieces of documentation but 
no luck so far. Can someone please point me to a document or tutorial 
that explains how this is currently done in Galaxy and also any 
issues/gaps that may be worth addressing?


I am also generally interested in how Galaxy works "under the hood". 
Is there a document that explains the architecture and design?


Many thanks in advance!

Sally.


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--
Jennifer Hillman-Jackson
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Re: [galaxy-dev] Cannot access saved history nor saved datasets

[Jennifer Jackson]

Hi Joshua,

If you are still having issues, you'll want to contact the folks running 
that specific instance for support. They'll know the state of the 
server. See this link, under the section "User Support" for their google 
group contact:

https://wiki.galaxyproject.org/PublicGalaxyServers#Cistrome_Analysis_Pipeline

Best,

Jen
Galaxy team

On 5/1/14 12:01 PM, Joshua David Aaker wrote:
I am able to use my current history and run tools but I can't move 
away nor create new histories.


I am currently using the Cistrome instance of Galaxy.

Here is the error I receive:


  Internal Server Error


Galaxy was unable to successfully complete your request

URL: http://cistrome.org/ap/history/list
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:*132* in |__call__|
|>> *return* 
self*.*handle_request*(* environ*,* start_response *)*|

Module galaxy.web.framework.base:*190* in |handle_request|
|>> body *=* method*(* trans*,* 
kwargs *)*|

Module galaxy.web.framework:*98* in |decorator|
|>> *return* func*(* self*,* 
trans*,* ***args*,* kwargs *)*|

Module galaxy.webapps.galaxy.controllers.history:*294* in |list|
|>> *return* 
self*.*stored_list_grid*(* trans*,* status*=*status*,* 
message*=*message*,* kwargs *)*|

Module galaxy.web.framework.helpers.grids:*209* in |__call__|
|>> total_num_rows *=* 
query*.*count*(**)*|

Module sqlalchemy.orm.query:*2571* in |count|
Module sqlalchemy.orm.query:*2215* in |scalar|
Module sqlalchemy.orm.query:*2184* in |one|
Module sqlalchemy.orm.query:*2227* in |__iter__|
Module sqlalchemy.orm.query:*2242* in |_execute_and_instances|
Module sqlalchemy.engine.base:*1449* in |execute|
Module sqlalchemy.engine.base:*1584* in |_execute_clauseelement|
Module sqlalchemy.engine.base:*1698* in |_execute_context|
Module sqlalchemy.engine.base:*1691* in |_execute_context|
Module sqlalchemy.engine.default:*331* in |do_execute|
Module MySQLdb.cursors:*173* in |execute|
Module MySQLdb.connections:*36* in |defaulterrorhandler|
*OperationalError: (OperationalError) (1030, 'Got error 28 from 
storage engine') 'SELECT count(*) AS count_1 \nFROM (SELECT history.id 
AS history_id, history.create_time AS history_create_time, 
history.update_time AS history_update_time, history.user_id AS 
history_user_id, history.name AS history_name, history.hid_counter AS 
history_hid_counter, history.deleted AS history_deleted, 
history.purged AS history_purged, history.importing AS 
history_importing, history.genome_build AS history_genome_build, 
history.importable AS history_importable, history.slug AS 
history_slug, history.published AS history_published \nFROM history 
\nWHERE history.importing = %s AND %s = history.user_id AND 
history.deleted = %s ORDER BY history.update_time DESC) AS anon_1' (0, 
1889L, 0)*


Any suggestions or more information you need?

-Josh


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--
Jennifer Hillman-Jackson
http://galaxyproject.org

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Re: [galaxy-dev] Galaxy REST API: multiple params per tool

[Jim McCusker]

It looks like this is already the case, but only documented in the code
(lib/galaxy/webapps/galaxy/api/workflows.py):

def _update_step_parameters(step, param_map):
"""
Update ``step`` parameters based on the user-provided ``param_map``
dict.

``param_map`` should be structured as follows::

  PARAM_MAP = {STEP_ID: PARAM_DICT, ...}
  PARAM_DICT = {NAME: VALUE, ...}

For backwards compatibility, the following (deprecated) format is
also supported for ``param_map``::

  PARAM_MAP = {TOOL_ID: PARAM_DICT, ...}

in which case PARAM_DICT affects all steps with the given tool id.
If both by-tool-id and by-step-id specifications are used, the
latter takes precedence.

Finally (again, for backwards compatibility), PARAM_DICT can also
be specified as::

  PARAM_DICT = {'param': NAME, 'value': VALUE}

Note that this format allows only one parameter to be set per step.
"""

Thanks,
Jim


On Mon, May 5, 2014 at 1:56 PM, Jim McCusker wrote:

> The current method for supplying parameters to tools using the REST API
> for workflows is fairly broken. The structure is as follow:
>
>   "parameters":{
> "tool_1": {
> "param":"param_name",
> "value":"param value"
> },
> "tool_2": {
> "param":"param_name",
> "value":"param value"
> }
>
> This structure means that it is impossible to submit more than 1 parameter
> per tool within a workflow. Tools themselves, and workflows that use them,
> have no problems with accepting multiple parameters. We should be
> supporting something more like the following:
>
>   "parameters":{
> "tool_1": {
> "param_name1":"param value 1"
> "param_name2":"param value 2"
> },
> "tool_2": {
> "tool_2_param_name1":"param value 1"
> "tool_2_param_name2":"param value 2"
> }
>
> Is there any work towards something like this taking place? I imagine that
> the REST API could support both formats (if the tool parameters dict has
> anything in it other than "param" and "value", use the new structure) for
> backwards compatibility.
>
> Thanks,
> Jim
>
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[galaxy-dev] Galaxy REST API: multiple params per tool

[Jim McCusker]

The current method for supplying parameters to tools using the REST API for
workflows is fairly broken. The structure is as follow:

  "parameters":{
"tool_1": {
"param":"param_name",
"value":"param value"
},
"tool_2": {
"param":"param_name",
"value":"param value"
}

This structure means that it is impossible to submit more than 1 parameter
per tool within a workflow. Tools themselves, and workflows that use them,
have no problems with accepting multiple parameters. We should be
supporting something more like the following:

  "parameters":{
"tool_1": {
"param_name1":"param value 1"
"param_name2":"param value 2"
},
"tool_2": {
"tool_2_param_name1":"param value 1"
"tool_2_param_name2":"param value 2"
}

Is there any work towards something like this taking place? I imagine that
the REST API could support both formats (if the tool parameters dict has
anything in it other than "param" and "value", use the new structure) for
backwards compatibility.

Thanks,
Jim
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Dannon Baker]

If they're fetching as it runs the tests, you may not need to do it up
front explicitly.  It's worth noting, though, that this is how galaxy
normally runs (checking for and fetching eggs up front -- except when using
the --stop-daemon argument) under run.sh.


On Mon, May 5, 2014 at 11:15 AM, Peter Cock wrote:

> On Mon, May 5, 2014 at 3:47 PM, Dannon Baker 
> wrote:
> > On Mon, May 5, 2014 at 10:32 AM, Peter Cock 
> > wrote:
> >>
> >> However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
> >> the old error persists. Is there a case-sensitivity issue here (PyYAML
> >> versus pyyaml)?
> >
> > Yep, I've adjusted that now and my guess is it'll work next time.
> >
> > Let me know if it doesn't, and thanks for finding the issue!
>
> Green light :)
> https://travis-ci.org/peterjc/pico_galaxy/builds/24456751
>
> I'm checking if I actually did need the fetch eggs or not...
>
> Thank you,
>
> Peter
>
> (Apologies for previous blank email, slip of the mouse)
>
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Peter Cock]

On Mon, May 5, 2014 at 3:47 PM, Dannon Baker  wrote:
> On Mon, May 5, 2014 at 10:32 AM, Peter Cock 
> wrote:
>>
>> However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
>> the old error persists. Is there a case-sensitivity issue here (PyYAML
>> versus pyyaml)?
>
> Yep, I've adjusted that now and my guess is it'll work next time.
>
> Let me know if it doesn't, and thanks for finding the issue!

Green light :)
https://travis-ci.org/peterjc/pico_galaxy/builds/24456751

I'm checking if I actually did need the fetch eggs or not...

Thank you,

Peter

(Apologies for previous blank email, slip of the mouse)
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Peter Cock]

On Mon, May 5, 2014 at 3:47 PM, Dannon Baker  wrote:
> On Mon, May 5, 2014 at 10:32 AM, Peter Cock 
> wrote:
>>
>> However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
>> the old error persists. Is there a case-sensitivity issue here (PyYAML
>> versus pyyaml)?
>
>
> Yep, I've adjusted that now and my guess is it'll work next time.
>
> Let me know if it doesn't, and thanks for finding the issue!
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Dannon Baker]

On Mon, May 5, 2014 at 10:32 AM, Peter Cock wrote:

> However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
> the old error persists. Is there a case-sensitivity issue here (PyYAML
> versus pyyaml)?
>

Yep, I've adjusted that now and my guess is it'll work next time.

Let me know if it doesn't, and thanks for finding the issue!
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Re: [galaxy-dev] Bam upload fails: samtools not found

[Peter Cock]

On Mon, May 5, 2014 at 3:30 PM, Geert Vandeweyer
 wrote:
> Hi,
>
> I'm having issues uploading bam files to our galaxy server. It fails for
> both FTP and browser upload. Upload.py is executed on the local job runner.
>
> The error is:
>
> Traceback (most recent call last):
>   File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 390, in
> 
> __main__()
>   File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 379, in
> __main__
> add_file( dataset, registry, json_file, output_path )
>   File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in
> add_file
> if link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ):
>   File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 144, in
> dataset_content_needs_grooming
> version = self._get_samtools_version()
>   File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 128, in
> _get_samtools_version
> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
>   File "/usr/lib/python2.6/subprocess.py", line 633, in __init__
> errread, errwrite)
>   File "/usr/lib/python2.6/subprocess.py", line 1139, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
>
> The logs show 'galaxy.tools.deps WARNING 2014-05-05 15:39:20,676 Failed to
> resolve dependency on 'samtools', ignoring'
>
>
> I do have samtools in my path (~/bin/samtools).

Is samtools on the Galaxy user's $PATH not just your personal account?
i.e. Dd you log in as Galaxy to check this?

Peter
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Peter Cock]

Change made:
https://github.com/peterjc/pico_galaxy/commit/19d24c71b5c24cb908907f25e5d992627165736c
https://travis-ci.org/peterjc/pico_galaxy/builds/24455410

That worked in one sense:

$ python scripts/fetch_eggs.py
Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg
Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.3-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/bx_python/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-1.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.12-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg
Fetched 
http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg
Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/PyYAML/PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
Fetched 
http://eggs.galaxyproject.org/SQLAlchemy/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg
Fetched 
http://eggs.galaxyproject.org/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/poster/poster-0.8.1-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/MarkupSafe/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
Fetched http://eggs.galaxyproject.org/Routes/Routes-1.12.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/pycrypto/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg
Fetched 
http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/wsgiref/wsgiref-0.1.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg
Fetched http://eggs.galaxyproject.org/pytz/pytz-2013.9-py2.7.egg
Fetched http://eggs.galaxyproject.org/nose/nose-0.11.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/requests/requests-2.2.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/anyjson/anyjson-0.3.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebError/WebError-0.8a-py2.7.egg
Fetched http://eggs.galaxyproject.org/twill/twill-0.9-py2.7.egg

However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
the old error persists. Is there a case-sensitivity issue here (PyYAML
versus pyyaml)?

...

functional_tests.py INFO 2014-05-05 14:23:11,383 Embedded Universe
application started
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,385 Enabling
'error' controller, class: Error
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,386 Enabling
'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,432 Enabling
'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,438 Enabling
'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,440 Enabling
'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,489 Enabling
'library' controller, class: Library
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,490 Enabling
'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling
'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2014-

[galaxy-dev] Bam upload fails: samtools not found

[Geert Vandeweyer]

Hi,

I'm having issues uploading bam files to our galaxy server. It fails for 
both FTP and browser upload. Upload.py is executed on the local job runner.


The error is:

Traceback (most recent call last):
  File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 390, in 
__main__()
  File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 379, in __main__
add_file( dataset, registry, json_file, output_path )
  File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 144, in 
dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 128, in 
_get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, 
stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib/python2.6/subprocess.py", line 633, in __init__
errread, errwrite)
  File "/usr/lib/python2.6/subprocess.py", line 1139, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory


The logs show 'galaxy.tools.deps WARNING 2014-05-05 15:39:20,676 Failed to 
resolve dependency on 'samtools', ignoring'


I do have samtools in my path (~/bin/samtools).

Also, the file is actually uploaded fine (can be downloaded again correctly), 
but cannot be used in galaxy due to its 'error' state.

Any advice on how to solve this?

Best,

Geert


--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Dannon Baker]

Can you add a `python scripts/fetch_eggs.py` to your travis config just
after the stop-daemon?  That should parse eggs.ini and fetch all of the
eggs.


On Mon, May 5, 2014 at 9:51 AM, Peter Cock wrote:

> On Mon, May 5, 2014 at 2:30 PM, Dannon Baker 
> wrote:
> > Hey Peter,
> >
> > Just looking at the travis job, it looks like there's not a fetch_eggs
> step
> > at the start, but rather that it's fetching as they're require()'d.  Is
> that
> > correct?
>
> Yes, https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml
> does not (currently) attempt to fetch any eggs explicitly - it lets the
> different bits of Galaxy do this on demand.
>
> Is there a simple command line instruction to tell Galaxy to fetch
> all the eggs it might want?
>
> > In any event, I'm changing the order of those requires in
> > 13302:92519a9bfa32, which may resolve your issue.  They work fine like
> that
> > in production with eggs fetched ahead of time, but I could see how that'd
> > cause the failure you're seeing.
>
>
> https://bitbucket.org/galaxy/galaxy-central/commits/92519a9bfa32a42ce47a63fdb72c8e2d717ec52e
>
> It looks like John has his Galaxy mirror automatically updates (or he
> did a push just now), so I could ask TravisCI to retest immediately.
> [In earlier testing GitHub was faster than BitBucket for fetching Galaxy]:
>
>
> https://github.com/jmchilton/galaxy-central/commit/9e72c14ef176e494a611bee6441477a05fb8e677
>
> Unfortunately, no real change:
>
> ...
> functional_tests.py INFO 2014-05-05 13:44:46,611 Embedded Universe
> application started
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,684 Enabling
> 'requests' controller, class: Requests
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,685 Enabling
> 'requests_common' controller, class: RequestsCommon
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,758 Enabling
> 'library_common' controller, class: LibraryCommon
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,762 Enabling
> 'library' controller, class: Library
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,765 Enabling
> 'userskeys' controller, class: User
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,773 Enabling
> 'tool_runner' controller, class: ToolRunner
> galaxy.eggs DEBUG 2014-05-05 13:44:46,958 Fetched
> http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling
> 'admin_toolshed' controller, class: AdminGalaxy
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling
> 'admin_toolshed' controller, class: AdminToolshed
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,189 Enabling
> 'dataset' controller, class: DatasetInterface
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,190 Enabling
> 'search' controller, class: SearchController
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,202 Enabling
> 'data_admin' controller, class: DataAdmin
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,246 Enabling
> 'user' controller, class: User
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,256 Enabling
> 'external_service' controller, class: ExternalService
> galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,260 Enabling
> 'ucsc_proxy' controller, class: UCSCProxy
> Traceback (most recent call last):
>   File "./scripts/functional_tests.py", line 601, in 
> sys.exit( main() )
>   File "./scripts/functional_tests.py", line 417, in main
> use_translogger=False, static_enabled=STATIC_ENABLED )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py",
> line 49, in app_factory
> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py",
> line 441, in add_ui_controllers
> module = import_module( module_name )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py",
> line 37, in import_module
> __import__(name)
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
> line 18, in 
> eggs.require('pyyaml')
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 412, in require
> return pkg_resources.working_set.require( req_str )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
> line 666, in require
> needed = self.resolve(parse_requirements(requirements))
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
> line 565, in resolve
> raise DistributionNotFound(req)  # XXX put more info here
> pkg_resources.DistributionNotFound: pyyaml
> galaxy.jobs.handler INFO 2014-05-05 13:44:47,295 sending stop signal
> to worker thread
> galaxy.jobs.handler INFO 2014-05-05 13:44:47,296 job handler que

Re: [galaxy-dev] File upload error

[Dannon Baker]

Are you using usegalaxy.org?

This generally indicates a temporary error with one of our cluster node (if
using usegalaxy.org), or a misconfiguration of the job management system if
you're seeing this on a local cluster.  If you're using usegalaxy.org I'd
recommend simply retrying the upload.

-Dannon


On Sat, May 3, 2014 at 4:21 PM, Heller Gerwin <
gerwin.hel...@meduniwien.ac.at> wrote:

> Hello!
>
> I tried to upload some file to Galaxy but received th error "Job output
> not returned from cluster". I got it for the first time, file upload always
> worked in the past.
> What can I do?
>
> Thanks for help, Gerwin
>
> --
> Gerwin Heller, Ph.D.
> Medical University of Vienna
> Department of Medicine I
> Division of Oncology
> Währinger Gürtel 18-20
> A-1090 Vienna, Austria
> Phone: +43 1 40400 4433
> Fax: +43 1 40400 4451
> ___
> 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:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Peter Cock]

On Mon, May 5, 2014 at 2:30 PM, Dannon Baker  wrote:
> Hey Peter,
>
> Just looking at the travis job, it looks like there's not a fetch_eggs step
> at the start, but rather that it's fetching as they're require()'d.  Is that
> correct?

Yes, https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml
does not (currently) attempt to fetch any eggs explicitly - it lets the
different bits of Galaxy do this on demand.

Is there a simple command line instruction to tell Galaxy to fetch
all the eggs it might want?

> In any event, I'm changing the order of those requires in
> 13302:92519a9bfa32, which may resolve your issue.  They work fine like that
> in production with eggs fetched ahead of time, but I could see how that'd
> cause the failure you're seeing.

https://bitbucket.org/galaxy/galaxy-central/commits/92519a9bfa32a42ce47a63fdb72c8e2d717ec52e

It looks like John has his Galaxy mirror automatically updates (or he
did a push just now), so I could ask TravisCI to retest immediately.
[In earlier testing GitHub was faster than BitBucket for fetching Galaxy]:

https://github.com/jmchilton/galaxy-central/commit/9e72c14ef176e494a611bee6441477a05fb8e677

Unfortunately, no real change:

...
functional_tests.py INFO 2014-05-05 13:44:46,611 Embedded Universe
application started
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,684 Enabling
'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,685 Enabling
'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,758 Enabling
'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,762 Enabling
'library' controller, class: Library
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,765 Enabling
'userskeys' controller, class: User
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,773 Enabling
'tool_runner' controller, class: ToolRunner
galaxy.eggs DEBUG 2014-05-05 13:44:46,958 Fetched
http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling
'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling
'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,189 Enabling
'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,190 Enabling
'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,202 Enabling
'data_admin' controller, class: DataAdmin
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,246 Enabling
'user' controller, class: User
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,256 Enabling
'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,260 Enabling
'ucsc_proxy' controller, class: UCSCProxy
Traceback (most recent call last):
  File "./scripts/functional_tests.py", line 601, in 
sys.exit( main() )
  File "./scripts/functional_tests.py", line 417, in main
use_translogger=False, static_enabled=STATIC_ENABLED )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py",
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py",
line 441, in add_ui_controllers
module = import_module( module_name )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py",
line 37, in import_module
__import__(name)
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
line 18, in 
eggs.require('pyyaml')
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
line 412, in require
return pkg_resources.working_set.require( req_str )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
line 666, in require
needed = self.resolve(parse_requirements(requirements))
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
line 565, in resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: pyyaml
galaxy.jobs.handler INFO 2014-05-05 13:44:47,295 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2014-05-05 13:44:47,296 job handler queue stopped
...

Peter
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Re: [galaxy-dev] specify file_path for each Galaxy registered users

[Dannon Baker]

Hey Weiyan,

You can't (currently) specify disk destinations per user, but you can
certainly use multiple disks in a pool.  For one example, see the sample
object store configuration here (and also in your galaxy distribution):
https://bitbucket.org/galaxy/galaxy-central/src/92519a9bfa32a42ce47a63fdb72c8e2d717ec52e/object_store_conf.xml.sample?at=default

There isn't currently formal documentation for this (that I could find just
now), but I'm happy to help if you run into any issues.

-Dannon


On Sat, May 3, 2014 at 11:32 PM, Weiyan Shen  wrote:

> Galaxy developers:
> We can set the *file_path *in universe_wsgi.ini to specify the saved
> Galaxy results.But whether it is possible for us to specify *file_path*for 
> each Galaxy registered users,for which multi-hard disks can be used
> effectively in some ways?
> Thank you very much for any help.
>
> Regards,Weiyan
>
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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[galaxy-dev] File upload error

[Heller Gerwin]

Hello!

I tried to upload some file to Galaxy but received th error "Job output 
not returned from cluster". I got it for the first time, file upload 
always worked in the past.

What can I do?

Thanks for help, Gerwin

--
Gerwin Heller, Ph.D.
Medical University of Vienna
Department of Medicine I
Division of Oncology
Währinger Gürtel 18-20
A-1090 Vienna, Austria
Phone: +43 1 40400 4433
Fax: +43 1 40400 4451
___
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 http://lists.bx.psu.edu/

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 http://galaxyproject.org/search/mailinglists/

[galaxy-dev] specify file_path for each Galaxy registered users

[Weiyan Shen]

Galaxy developers:
We can set the file_path in universe_wsgi.ini to specify the saved Galaxy 
results.But whether it is possible for us to specify file_path for each Galaxy 
registered users,for which multi-hard disks can be used effectively in some 
ways?
Thank you very much for any help.


Regards,Weiyan___
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Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Dannon Baker]

Hey Peter,

Just looking at the travis job, it looks like there's not a fetch_eggs step
at the start, but rather that it's fetching as they're require()'d.  Is
that correct?  In any event, I'm changing the order of those requires
in 13302:92519a9bfa32, which may resolve your issue.  They work fine like
that in production with eggs fetched ahead of time, but I could see how
that'd cause the failure you're seeing.

-Dannon


On Mon, May 5, 2014 at 9:14 AM, Peter Cock wrote:

> Hi all,
>
> Recently my TravisCI tests have started failing during the tool
> functional tests due to what looks like a missing dependency:
> e.g. https://travis-ci.org/peterjc/pico_galaxy/jobs/2682
>
> ...
> galaxy.eggs DEBUG 2014-05-05 11:26:47,387 Fetched
> http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg
> galaxy.eggs DEBUG 2014-05-05 11:26:47,753 Fetched
> http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
> Traceback (most recent call last):
>   File "./scripts/functional_tests.py", line 601, in 
> sys.exit( main() )
>   File "./scripts/functional_tests.py", line 417, in main
> use_translogger=False, static_enabled=STATIC_ENABLED )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py",
> line 49, in app_factory
> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py",
> line 441, in add_ui_controllers
> module = import_module( module_name )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py",
> line 37, in import_module
> __import__(name)
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
> line 20, in 
> eggs.require('pyyaml')
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 412, in require
> return pkg_resources.working_set.require( req_str )
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
> line 666, in require
> needed = self.resolve(parse_requirements(requirements))
>   File
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
> line 565, in resolve
> raise DistributionNotFound(req)  # XXX put more info here
> pkg_resources.DistributionNotFound: pyyaml
>
>
> Is there a missing egg declaration for pyyaml?
>
> I found this commit about a PyYAML 3.10 egg., perhaps linked?
>
> https://bitbucket.org/galaxy/galaxy-central/commits/c36dc4155beb0ae5e117ca33e0ad231535186d6d
>
> Thanks,
>
> Peter
> ___
> 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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[galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here

[Peter Cock]

Hi all,

Recently my TravisCI tests have started failing during the tool
functional tests due to what looks like a missing dependency:
e.g. https://travis-ci.org/peterjc/pico_galaxy/jobs/2682

...
galaxy.eggs DEBUG 2014-05-05 11:26:47,387 Fetched
http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg
galaxy.eggs DEBUG 2014-05-05 11:26:47,753 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Traceback (most recent call last):
  File "./scripts/functional_tests.py", line 601, in 
sys.exit( main() )
  File "./scripts/functional_tests.py", line 417, in main
use_translogger=False, static_enabled=STATIC_ENABLED )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py",
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py",
line 441, in add_ui_controllers
module = import_module( module_name )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py",
line 37, in import_module
__import__(name)
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
line 20, in 
eggs.require('pyyaml')
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
line 412, in require
return pkg_resources.working_set.require( req_str )
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
line 666, in require
needed = self.resolve(parse_requirements(requirements))
  File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py",
line 565, in resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: pyyaml


Is there a missing egg declaration for pyyaml?

I found this commit about a PyYAML 3.10 egg., perhaps linked?
https://bitbucket.org/galaxy/galaxy-central/commits/c36dc4155beb0ae5e117ca33e0ad231535186d6d

Thanks,

Peter
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