Re: [galaxy-dev] ncbi_blast_plus - tool shed updates

[Björn Grüning]

Hi Shantanu,

"updates" are a little bit special. They refer to a changeset of the
tool that is not invasive. For example if the tool number did not
change. If the change in will affect reproducibility it will get a new
"installable revision number". That new revision is only installable
with a new installation. Go to the toolshed select ncbi_blast_plus (new
revision) hit install. Done.

Here is the wiki page with more information:
http://wiki.galaxyproject.org/RepositoryRevisions

Hope that helps,
Bjoern 

> 
> 
> I am trying to get repository updates for the ncbi_blast_plus tool
> which is making following request to the toolshed site:
> 
> 
> http://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url=http://galaxydev.uabgrid.uab.edu/&name=ncbi_blast_plus&owner=devteam&changeset_revision=d375502056f1
> 
> 
> This request is coming back with following response with
> latest_changeset_revision  same as changeset_revision.
> 
> 
> http://localhost:5000/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=ncbi_blast_plus&owner=devteam&changeset_revision=d375502056f1&latest_changeset_revision=d375502056f1&latest_ctx_rev=0
> 
> 
> This results in following message in the browser: "The installed
> repository named 'ncbi_blast_plus' is current,  there are no updates
> available.". 
> 
> 
> The latest ncbi_blast_plus changeset revision in the toolshed is
> "9dabbfd73c8a", so I am not sure why above update request is coming
> back with d375502056f1 revision. 
> 
> 
> Any clues on what might be wrong here? Appreciate any further
> debugging steps.
> 
> 
> --
> Thanks,
> Shantanu
> ___
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[galaxy-dev] ncbi_blast_plus - tool shed updates

[Shantanu Pavgi (Campus)]

I am trying to get repository updates for the ncbi_blast_plus tool which is 
making following request to the 
toolshed
 site:

http://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url=http://galaxydev.uabgrid.uab.edu/&name=ncbi_blast_plus&owner=devteam&changeset_revision=d375502056f1

This request is coming back with following response with 
latest_changeset_revision  same as changeset_revision.

http://localhost:5000/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=ncbi_blast_plus&owner=devteam&changeset_revision=d375502056f1&latest_changeset_revision=d375502056f1&latest_ctx_rev=0

This results in following message in the browser: "The installed repository 
named 'ncbi_blast_plus' is current,  there are no updates available.".

The latest ncbi_blast_plus changeset revision in the toolshed is 
"9dabbfd73c8a", so I am not sure why above update request is coming back with 
d375502056f1 revision.

Any clues on what might be wrong here? Appreciate any further debugging steps.

--
Thanks,
Shantanu
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Re: [galaxy-dev] Manhattan/qq plots

[Ross]

Hi, Thomas.

There are no resources available to support that now 3 year old rgenetics
code so I'm sad but not surprised to hear of this new problem.
The grant ended long ago and I no longer work with SNP so have no excuse to
keep fixing or working on it.

Is someone using this code willing to take it over, fix these kinds of bugs
and add automated installation to bring it up to speed ? I'll help all I
can but without a volunteer, the code should be considered deprecated and
will soon disappear from the distribution.


On Tue, Aug 27, 2013 at 2:14 AM, Bjoern Gruening
wrote:

> Hi Thomas,
>
> I think you are running a to new version of gplot
>
> http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/
>
> opts is now deprecated and likely causes that error. Can you downgrade
> the gplot version?
> We are working on a R dependencies mechanism but we are not done yet,
> sorry.
>
> Hope that helps,
> Bjoern
>
> > Hey guys,
> >
> >
> >
> > we are running a local galaxy instance (10200:fd4113962c32)with R
> > version 3.0.1 and want to use Manhattan/qq, but we are missing the
> > pval manhatan.pdf, only pval qqplot.pdf is generated and we are
> > getting the following error:
> >
> >
> >
> > Nonzero exit code = 1
> >
> > [1] "### 11008 values read
> > from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read
> > - now running plots"
> >
> >
> >
> > 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in
> > version 0.9.1)
> >
> >
> >
> > Setting the plot title with opts(title="...") is deprecated.
> >
> >
> >
> > Use labs(title="...") or ggtitle("...") instead. (Deprecated; last
> > used in version 0.9.1)
> >
> >
> >
> > Scale for 'x' is already present. Adding another scale for 'x', which
> > will replace the existing scale.
> >
> >
> >
> > Scale for 'y' is already present. Adding another scale for 'y', which
> > will replace the existing scale.
> >
> >
> >
> > [1] "## qqplot on pval done"
> >
> >
> >
> > [1] "## manhattan on pval starting 1 2 3"
> >
> >
> >
> > Error in structure(list(call = match.call(), aesthetics =
> > aesthetics,  :
> >
> >
> >
> >   argument "values" is missing, with no default
> >
> >
> >
> > Calls: rgqqMan ... scale_colour_manual -> manual_scale ->
> > discrete_scale -> structure
> >
> >
> >
> > Execution halted
> >
> >
> >
> >
> >
> > At the galaxy-main ist working without any problems using the same
> > input file.
> >
> > All the necessary packages should be installed.
> >
> >
> >
> > Any ideas? Thanks for your help.
> >
> >
> >
> > Thomas
> >
> >
> > ___
> > 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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>



-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4J
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Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

[Björn Grüning]

Hi Dave,

I can confirm that it is also working for me.

uname -a
Linux threonin 3.5.0-36-generic #57-Ubuntu SMP Wed Jun 19 15:10:49 UTC
2013 x86_64 x86_64 x86_64 GNU/Linux
bag@threonin:~/projects/github/galaxytools$ arch
x86_64
bag@threonin:~/projects/github/galaxytools$ echo $0
bash

Is the toolshed somehow running in chroot or so?
Dave can you grep through the log file and can have a look why the
dependency shell is not build correctly?

Thanks,
Bjoern


> Peter,
> 
> I apologize for the delay, here is the information you requested:
> 
> ubuntu@ip-10-0-0-243:~$ uname -a
> Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 
> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> ubuntu@ip-10-0-0-243:~$ arch
> x86_64
> ubuntu@ip-10-0-0-243:~$ echo $0
> -bash
> 
> --Dave B.
> 
> On 08/26/2013 09:44 AM, Peter Cock wrote:
> > (Off list)
> >
> > Hi Dave, Greg,
> >
> > Just a reminder - without a bit more information about the Tool Shed
> > cluster I am stuck about how to debug this install issue.
> >
> > Thanks,
> >
> > Peter
> >
> >
> > On Wed, Aug 21, 2013 at 2:05 PM, Peter Cock  
> > wrote:
> >> On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier  wrote:
> >>> Peter,
> >>>
> >>> Here is the relevant log output for the installation of ncbi_blast_plus. A
> >>> quick google informs me that exit code 64 means "command line usage 
> >>> error",
> >>> for what it's worth.
> >>>
> >>> ...
> >>> tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new 
> >>> row
> >>> (or updating an existing row) for repository 'package_blast_plus_2_2_26' 
> >>> in
> >>> the tool_shed_repository table, status set to 'New'.
> >>>
> >>> Warning: local() encountered an error (return code 64) while executing '
> >>>  if [[ "$(uname)" == "Linux" ]]; then export
> >>> FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi &&
> >>>  if [[ "$(arch)" == "x86_64" ]]; then export
> >>> FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi &&
> >>>  if [[ "$(uname)" == "Darwin" ]]; then export
> >>> FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi &&
> >>>  echo Fetching $FILENAME &&
> >>>  if [[ "$(uname)" == "Linux" ]]; then wget
> >>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi 
> >>> &&
> >>>  if [[ "$(uname)" == "Darwin" ]]; then curl -O
> >>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi 
> >>> &&
> >>>  tar -zxvf $FILENAME &&
> >>>  echo Downloaded and decompressed
> >>>  '
> >>>
> >>
> >> Thanks Dave,
> >>
> >> I've made a note on this Trello card about exposing the log information
> >> of unsuccessful builds on the Tool Shed,
> >> https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages
> >>
> >> Can you tell me what version of Linux this is, and which shell?
> >>
> >> $ uname
> >> ...
> >>
> >> $ arch
> >> ...
> >>
> >> $ echo $0
> >> ...
> >>
> >> That might give me a clue about the nature of the failure. My
> >> hunch is that I am using something bash specific.
> >>
> >> The simplest solution would be if you could run each of these
> >> command by hand to see if it triggers the same error:
> >>
> >> if [[ "$(uname)" == "Linux" ]]; then export 
> >> FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi
> >> if [[ "$(arch)" == "x86_64" ]]; then export 
> >> FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi
> >> if [[ "$(uname)" == "Darwin" ]]; then export 
> >> FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi
> >> echo Fetching $FILENAME
> >> if [[ "$(uname)" == "Linux" ]]; then wget 
> >> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
> >> if [[ "$(uname)" == "Darwin" ]]; then curl -O 
> >> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
> >> tar -zxvf $FILENAME
> >> echo Downloaded and decompressed
> >>
> >> Thanks,
> >>
> >> Peter



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Re: [galaxy-dev] Login hook

[Maddhi, Srinivas]

Hi Adam,

I appreciate your taking the time to provide detailed inputs along with
links to relevant posts.


Our instance is currently set up to allow users to self-service account
provisioning in that if they are are a member of the University and have
an appropriate entry in our LDAP/AD system, the act of providing their
authentication credentials at the Galaxy login prompt results in the
Galaxy account and a local OS-level "account" (only used for sFTP) being
provisioned automagically via the aforementioned script invoked from a
modified version of ../lib/galaxy/web/framework/__init__.py creating a
local account and the requisite FTP upload directory if those don't
already exist. 

As you rightly pointed out keeping code customizations current with
upgrades is non-trivial and something I would like to minimize, and
therefore this post.

At this juncture, I will pursue the Shell/Python script polling
"galaxy_user" option or re-attempt the ProFTPD (which appears to not
require the creation of a local user account and has the ability to query
the PostgreSQL DB for user credentials; in our case the credentials would
have to be put together from a combination of PostgreSQL and LDAP queries)
option.

Thank you.

-Original Message-
From: Adam Brenner 
Date: Monday, August 26, 2013 12:45 PM
To: Srinivas Maddhi 
Cc: Galaxy Dev 
Subject: Re: [galaxy-dev] Login hook

>I am not aware of Galaxy having any sort of login hook as you
>described --- without writing custom code. This brings up the added
>challenge of keeping your custom modifications current with the latest
>release of galaxy.
>
>Another approach, and I am not sure how feasible this is on your
>setup, is to create all these added services during the user
>creation[1] process. On our HPC cluster this is the method we
>implemented. All our users can use SFTP, rsync, BBCP, etc to upload to
>the cluster and the user moves their data to galaxy by the "FTP
>Trick[2]" to their "dropbox" folder that galaxy has access to. Once
>data is moved to the dropbox folder, users login via the galaxy web
>interface and select the data via the Get Data -> Upload File
>interface.
>
>This might be a simpler approach, create these services for each new
>user during their account creation. You will be forced to use the
>command line interface to create new users, but I believe its far
>simpler then using postgres notify or the other methods you described.
>
>[1]: 
>http://dev.list.galaxyproject.org/user-creation-using-API-td4657726.html
>[2]: 
>http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271
>.html
>
>--
>Adam Brenner
>Computer Science, Undergraduate Student
>Donald Bren School of Information and Computer Sciences
>
>Research Computing Support
>Office of Information Technology
>http://www.oit.uci.edu/rcs/
>
>University of California, Irvine
>www.ics.uci.edu/~aebrenne/
>aebre...@uci.edu
>
>
>On Sun, Aug 25, 2013 at 9:39 AM, Maddhi, Srinivas
> wrote:
>> Hello,
>>
>> Does Galaxy provide a post-login hook that could be used to trigger an
>> operating system level action upon successful login ?
>>
>> Here is the scenario and use-case where that would come in handy:
>> * Local instance of Galaxy (Nov 2012 release) on a Linux server with a
>> PostgreSQL DB
>> * Upload via FTP feature is enabled
>> * Users are authenticated via LDAP and nginx
>> * Users should be able to securely upload files (to their sub-directory
>> within the configured FTP upload directory)
>>
>> The current method being employed to fulfill this use-case is through a
>> modification to Š/galaxy-dist/lib/galaxy/web/framework/__init__.py file
>> that calls a a shell script which creates an OS-level user and
>>associated
>> FTP upload directory.  Files are uploaded by users via sFTP (SSHD
>> configured to restrict Galaxy users to a chroot'ed directory).
>>
>> Options considered:
>> * Shell/Python script that periodically queries the "galaxy_user" table
>> and creates an OS-level user and FTP upload directory (not yet tried;
>> introduces delay between user creation and FTP capability unless
>>frequency
>> of polling is high)
>> * ProFTPD with sFTP and LDAP modules (increased administrative overhead
>> compared to using built-in SSHD; wasn't able to get auto directory
>> creation to work due to TBD cause)
>> * PostgreSQL listen-notify to call a sFTP user creation script when an
>> insert occurs in the "galaxy_user" table (not yet tried)
>>
>>
>> Thank you.
>>
>> --
>> Senior Systems Administrator
>> Iowa Institute for Human Genetics
>> ITS Research Services, The University of Iowa
>>
>>
>> ___
>> 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/

Re: [galaxy-dev] TS API installation broken

[Björn Grüning]

Thanks Dave,

any change we can get fix into the Tool Shed as well?

Cheers,
Bjoern

> Björn,
> 
> Thank you for the report, which revealed that there was another place 
> where this error was occurring. It has been fixed in 10447:e97f613a4948, 
> and that revision is now running on the test tool shed.
> 
> --Dave B.
> 
> On 08/26/2013 08:38 AM, Dave Bouvier wrote:
> > Björn,
> >
> > This looks like an issue that was fixed in 10444:ab74f2d80173, can you
> > confirm that you are running that revision or later locally?
> >
> > --Dave B.
> >
> > On 08/26/2013 07:46 AM, Bjoern Gruening wrote:
> >> Hi,
> >>
> >> if I try to install a repository via API I get the following error:
> >>
> >> Traceback (most recent call last):
> >>File
> >> "/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py",
> >> line 189, in decorator
> >>  rval = func( self, trans, *args, **kwargs)
> >>File
> >> "/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
> >> line 265, in install_repository_revision
> >>  tool_shed_repository_dict =
> >> tool_shed_repository.as_dict(
> >> value_mapper=default_tool_shed_repository_value_mapper( trans,
> >> tool_shed_repository ) )
> >>File
> >> "/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py",
> >> line 3350, in as_dict
> >>  return self.dictify( view='element', value_mapper=value_mapper )
> >>File
> >> "/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py",
> >> line 3445, in dictify
> >>  raise Exception( 'Unknown API view: %s' % view )
> >> Exception: Unknown API view: element
> >>
> >>
> >> Command line: python ./scripts/api/install_tool_shed_repositories.py
> >> --api f1326e8588535c628f03a0df517e2247 -l http://localhost:8080 --url
> >> http://toolshed.g2.bx.psu.edu/ -o devteam -r 4676e145a44e --name
> >> add_value
> >>
> >> Cheers,
> >> Bjoern
> >>
> >> ___
> >> 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/
> >>
> > ___
> > 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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> >
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> >



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Re: [galaxy-dev] Login hook

[Adam Brenner]

I am not aware of Galaxy having any sort of login hook as you
described --- without writing custom code. This brings up the added
challenge of keeping your custom modifications current with the latest
release of galaxy.

Another approach, and I am not sure how feasible this is on your
setup, is to create all these added services during the user
creation[1] process. On our HPC cluster this is the method we
implemented. All our users can use SFTP, rsync, BBCP, etc to upload to
the cluster and the user moves their data to galaxy by the "FTP
Trick[2]" to their "dropbox" folder that galaxy has access to. Once
data is moved to the dropbox folder, users login via the galaxy web
interface and select the data via the Get Data -> Upload File
interface.

This might be a simpler approach, create these services for each new
user during their account creation. You will be forced to use the
command line interface to create new users, but I believe its far
simpler then using postgres notify or the other methods you described.

[1]: http://dev.list.galaxyproject.org/user-creation-using-API-td4657726.html
[2]: 
http://dev.list.galaxyproject.org/user-names-with-authentication-td4659271.html

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Sun, Aug 25, 2013 at 9:39 AM, Maddhi, Srinivas
 wrote:
> Hello,
>
> Does Galaxy provide a post-login hook that could be used to trigger an
> operating system level action upon successful login ?
>
> Here is the scenario and use-case where that would come in handy:
> * Local instance of Galaxy (Nov 2012 release) on a Linux server with a
> PostgreSQL DB
> * Upload via FTP feature is enabled
> * Users are authenticated via LDAP and nginx
> * Users should be able to securely upload files (to their sub-directory
> within the configured FTP upload directory)
>
> The current method being employed to fulfill this use-case is through a
> modification to Š/galaxy-dist/lib/galaxy/web/framework/__init__.py file
> that calls a a shell script which creates an OS-level user and associated
> FTP upload directory.  Files are uploaded by users via sFTP (SSHD
> configured to restrict Galaxy users to a chroot'ed directory).
>
> Options considered:
> * Shell/Python script that periodically queries the "galaxy_user" table
> and creates an OS-level user and FTP upload directory (not yet tried;
> introduces delay between user creation and FTP capability unless frequency
> of polling is high)
> * ProFTPD with sFTP and LDAP modules (increased administrative overhead
> compared to using built-in SSHD; wasn't able to get auto directory
> creation to work due to TBD cause)
> * PostgreSQL listen-notify to call a sFTP user creation script when an
> insert occurs in the "galaxy_user" table (not yet tried)
>
>
> Thank you.
>
> --
> Senior Systems Administrator
> Iowa Institute for Human Genetics
> ITS Research Services, The University of Iowa
>
>
> ___
> 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] manage toolshed repos crashing

[Greg Von Kuster]

Hello Robert,

Is this still a problem?  If so, what version of Galaxy are you running?

Greg Von Kuster


On Aug 23, 2013, at 1:47 PM, Robert Baertsch  wrote:

> When I click on manage installed tool shed repos on the admin screen, I get 
> this error.
> 
> Any ideas how to debug?
> -Robert
> ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 26: 
> ordinal not in range(128)
> URL: http://su2c-dev.ucsc.edu/admin_toolshed/browse_repositories
> Module weberror.evalexception.middleware:364 in respond  view
> >>  app_iter = self.application(environ, detect_start_response)
> Module paste.recursive:84 in __call__  view
> >>  return self.application(environ, start_response)
> Module paste.httpexceptions:633 in __call__  view
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:132 in __call__  view
> >>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:190 in handle_request  view
> >>  body = method( trans, **kwargs )
> Module galaxy.web.framework:221 in decorator  view
> >>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:151 in 
> browse_repositories  view
> >>  return self.installed_repository_grid( trans, **kwd )
> Module galaxy.web.framework.helpers.grids:290 in __call__  view
> >>  kwargs=kwargs )
> Module galaxy.web.framework:991 in fill_template  view
> >>  return self.fill_template_mako( filename, **kwargs )
> Module galaxy.web.framework:1006 in fill_template_mako  view
> >>  return template.render( **data )
> Module mako.template:296 in render  view
> >>  return runtime._render(self, self.callable_, args, data)
> Module mako.runtime:660 in _render  view
> >>  **_kwargs_for_callable(callable_, data))
> Module mako.runtime:692 in _render_context  view
> >>  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> Module mako.runtime:718 in _exec_template  view
> >>  callable_(context, *args, **kwargs)
> Module _base_mako:42 in render_body  view
> >>  __M_writer(unicode(next.body()))
> Module _grid_base_mako:127 in render_body  view
> >>  __M_writer(unicode(self.grid_body( grid )))
> Module _grid_base_mako:747 in render_grid_body  view
> >>  __M_writer(unicode(self.make_grid( grid )))
> Module _grid_base_mako:777 in render_make_grid  view
> >>  __M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes )))
> Module _grid_base_mako:724 in render_render_grid_table  view
> >>  __M_writer(unicode(render_grid_table_body_contents( grid, 
> >> show_item_checkboxes )))
> Module _grid_base_mako:627 in render_grid_table_body_contents  view
> >>  return 
> >> render_render_grid_table_body_contents(context,grid,show_item_checkboxes)
> Module _grid_base_mako:335 in render_render_grid_table_body_contents  
> view
> >>  value = column.get_value( trans, grid, item )
> Module tool_shed.galaxy_install.grids.admin_toolshed_grids:61 in get_value
>   view
> >>  elif tool_shed_repository.missing_tool_dependencies:
> Module galaxy.model:3621 in missing_tool_dependencies  view
> >>  for tool_dependency in self.tool_dependencies:
> Module sqlalchemy.orm.attributes:168 in __get__  view
> Module sqlalchemy.orm.attributes:453 in get  view
> Module sqlalchemy.orm.strategies:508 in _load_for_state  view
> Module sqlalchemy.orm.strategies:574 in _emit_lazyload  view
> Module sqlalchemy.orm.query:2115 in all  view
> Module sqlalchemy.orm.query:2341 in instances  view
> Module sqlalchemy.engine.base:3204 in fetchall  view
> Module sqlalchemy.engine.base:3350 in _fetchall_impl  view
> UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 26: 
> ordinal not in range(128)
> 
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[galaxy-dev] 'galaxy-api-tools' project

[Carlos Borroto]

Hi,

I'm interested in developing a tool that would allow easy interaction
with the Galaxy API. I started coding and this[1] is what I have so
far.

[1]https://github.com/cjav/galaxy-api-tools

This is a pure "release early, release often" kind of project. In the
current state many of the project's goals are missing and current
implementation might significantly change. You can however already do
something like this:

$ galaxy-api-tools import --link --file-type fasta --library "API
Imports" --folder R_TEST --description "R_TEST with description."
--workflow 2491ee81eec9beee --extension .qual:qual454 --label
QUAL:.qual --label FASTA:.fna /local/data/R_TEST/1.fna
/local/data/R_TEST/2.fna

This will import(only '--link' not copy, copy is the default) these
two 454 fasta files with the matching quality files into data library
"API Imports" and folder "R_TEST"(it will create both if they don't
exists), it will them run a workflow where there are two inputs
labeled as FASTA and QUAL assigning the correct file to each, the
results will be available in a newly created history.

I shamelessly copied/adapted code from '$GALAXY_SOURCE/scripts/api'.
I'm releasing this code under BSD-Clause-2 which I think is one of the
most open license I could find in the github dropdown menu. Hopefully
this license won't have any incompatibility with Galaxy license which
seems very open also.

I would love to receive comments to help shape this tool. I'm very
open to any kind of suggestions. Also, if there is any worry the name
of the tool my cause any confusion on the source, please let me know
and I'll be happy to change it.

Best
Carlos
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Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

[Thon de Boer]

Yeah, pretty sure I'm up to date.

 

$ hg branches

default10411:c42567f43aa7

stable 10408:6822f41bc9bb (inactive)

[svcbioinfo@srv160 gs]$ hg branch

stable

[svcbioinfo@srv160 gs]$ hg tip

changeset:   10411:c42567f43aa7

tag: tip

user:greg

date:Mon Aug 19 13:19:56 2013 -0400

summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.

 

[svcbioinfo@srv160 gs]$ hg incoming

warning: bitbucket.org certificate with fingerprint
24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified
(check hostfingerprints or web.cacerts config setting)

comparing with https://bitbucket.org/galaxy/galaxy-dist/

searching for changes

no changes found

 

$ hg update release_2013.08.12

0 files updated, 0 files merged, 0 files removed, 0 files unresolved

 

Should I just take "lib/galaxy/tools/actions/__init__.py " from a fresh
install?

 

Regards,

 

Thon

 

Thon deBoer Ph.D., Bioinformatics Guru 
California, USA |p: +1 (650) 799-6839  |m:  thondeb...@me.com
 

Public profile on LinkedIn
 

 

From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
Sent: Saturday, August 24, 2013 7:39 AM
To: Thon de Boer
Cc: 'Galaxy-dev Galaxy-dev'
Subject: Re: [galaxy-dev] Why does my trackster complain about not being
able to display BED files?

 

It appears you are missing some updates. This issue was fixed in this
changeset 9992:

 

--

changeset:   9992:7105c53139d4

branch:  stable

parent:  9990:f35c0441e374

user:jeremy goecks mailto:jeremy.goe...@emory.edu> >

date:Tue Jun 11 17:34:26 2013 -0400

files:   lib/galaxy/tools/actions/__init__.py

description:

Use len_file_path config option rather than hardcoded path for chromInfo
tool parameter.

--

 

You might have missed this changeset if you updated to the late June release
soon after it came out. However, it is definitely included in the August
release. Can you confirm that you're running the August release?

 

Thanks,

J.

 

 

On Aug 23, 2013, at 9:08 PM, Thon de Boer wrote:





Ofcourse I spoke too soon.

 

I get a problem in that the conversion of my dataset reports that it cannot
find the chromosome length files, even though trickster itself has no
problem showing it.

 

I looked at the problem script and it is showing below

 

It seems that the script is passed the path to the chromosome files like
this "tool-data/shared/ucsc/chrom/hg19-decoy.len"

 

This will clearly never work since this file is not relative to the working
directory..

SO somewhere a script forgets to add the ${GALAXY_DATA_DIR} or whatever that
parameter is...

 

I could probably hardcode the location of the tool-data directory, but I
don't think that should be the solution.

 

Why do I only have this issue? SHOULD I have hardcoded the location of
tool-data?

 

The universe_wgi.ini.sample file does not hardcode this.

 

Am I missing some updates?

 

Thanks,


Thon

 

#!/bin/sh

GALAXY_LIB="None"

if [ "$GALAXY_LIB" != "None" ]; then

if [ -n "$PYTHONPATH" ]; then

PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"

else

PYTHONPATH="$GALAXY_LIB"

fi

export PYTHONPATH

fi

TMPDIR=/mnt/ngs/analysis/svcgalaxy/DATATEST/TMP

export TMPDIR

 

cd /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916

grep -v '^#' /mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2288.dat
| sort -k1,1 |   bedtools genomecov -bg -split -i stdin
-gtool-data/shared/ucsc/chrom/hg19-decoy.len> temp.bg ;
bedGraphToBigWig temp.bg
tool-data/shared/ucsc/chrom/hg19-decoy.len/mnt/ngs/analysis/svcgalaxy/DATATE
ST/files/002/dataset_2315.dat; cd /mnt/ngs/analysis/svcgalaxy/galaxy-test;
/mnt/ngs/analysis/svcgalaxy/galaxy-test/set_metadata.sh
/mnt/ngs/analysis/svcgalaxy/DATATEST/files
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916 .
/mnt/ngs/analysis/svcgalaxy/galaxy-test/universe_wsgi.ini
/mnt/ngs/analysis/svcgalaxy/DATA/TMP/tmp2KAn7W
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy.j
son
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata
_in_HistoryDatasetAssociation_2551_XsCZer,/mnt/ngs/analysis/svcgalaxy/DATATE
ST/job_working_directory/001/1916/metadata_kwds_HistoryDatasetAssociation_25
51_iNUAr_,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/191
6/metadata_out_HistoryDatasetAssociation_2551_ZHhosg,/mnt/ngs/analysis/svcga
laxy/DATATEST/job_working_directory/001/1916/metadata_results_HistoryDataset
Association_2551_tqtiIX,,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_di
rectory/001/1916/metadata_override_HistoryDatasetAssociation_2551_MOfd8w

echo $? >
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1
916.ec

 

Regards,

 

Thon

 

Thon deBoer Ph.D., 

Re: [galaxy-dev] Manhattan/qq plots

[Bjoern Gruening]

Hi Thomas,

I think you are running a to new version of gplot

http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/

opts is now deprecated and likely causes that error. Can you downgrade
the gplot version?
We are working on a R dependencies mechanism but we are not done yet,
sorry.

Hope that helps,
Bjoern

> Hey guys,
> 
>  
> 
> we are running a local galaxy instance (10200:fd4113962c32)with R
> version 3.0.1 and want to use Manhattan/qq, but we are missing the
> pval manhatan.pdf, only pval qqplot.pdf is generated and we are
> getting the following error:
> 
>  
> 
> Nonzero exit code = 1
> 
> [1] "### 11008 values read
> from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read
> - now running plots"
> 
>  
> 
> 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in
> version 0.9.1)
> 
>  
> 
> Setting the plot title with opts(title="...") is deprecated.
> 
>  
> 
> Use labs(title="...") or ggtitle("...") instead. (Deprecated; last
> used in version 0.9.1)
> 
>  
> 
> Scale for 'x' is already present. Adding another scale for 'x', which
> will replace the existing scale.
> 
>  
> 
> Scale for 'y' is already present. Adding another scale for 'y', which
> will replace the existing scale.
> 
>  
> 
> [1] "## qqplot on pval done"
> 
>  
> 
> [1] "## manhattan on pval starting 1 2 3"
> 
>  
> 
> Error in structure(list(call = match.call(), aesthetics =
> aesthetics,  : 
> 
>  
> 
>   argument "values" is missing, with no default
> 
>  
> 
> Calls: rgqqMan ... scale_colour_manual -> manual_scale ->
> discrete_scale -> structure
> 
>  
> 
> Execution halted
> 
>  
> 
>  
> 
> At the galaxy-main ist working without any problems using the same
> input file.
> 
> All the necessary packages should be installed.
> 
>  
> 
> Any ideas? Thanks for your help.
> 
>  
> 
> Thomas
> 
> 
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Re: [galaxy-dev] tool_dependencies.xml format

[James Taylor]

On Mon, Aug 26, 2013 at 11:48 AM, John Chilton  wrote:

> I think it is interesting that there was push back on providing
> infrastructure (tool actions) for obtaining CBL from github and
> performing installs based on it because it was not in the tool shed
> and therefore less reproducible, but the team believes infrastructure
> should be put in place to support pypi.

Well, first, I'm not sure what "the team" believes, I'm stating what I
believe and engaging in a discussion with "the community". At some
point this should evolve into what we are actually going to do and be
codified in a spec as a Trello card, which is even then not set in
stone.

Second, I'm not suggesting we depend on PyPI. The nice thing about the
second format I proposed on galaxy-dev is that we can easily parse out
the URL and archive that file. Then someday we could provide a
fallback repository where if the PyPI URL no longer works we still
have it stored.

> I think we all value reproduciblity here, but we make different
> calculations on what is reproducible. I think in terms of implementing
> the ideas James has laid out or similar things I have proposed, it
> might be beneficial to have some final answers on what external
> resources are allowed - both for obtaining a Galaxy IUC gold star and
> for the tool shed providing infrastructure to support their usage.

My focus is ensuring that we can archive things that pass through the
toolshed. Tarballs from *anywhere* are easy enough to deal with.
External version control repositories are a bit more challenging,
especially when you are pulling just a particular file out, so that's
where things got a little hinky for me.

Since we don't have the archival mechanism in place yet anyway, this
is more a philosophical discussion and setting the right precedent.

And yes, keeping an archive of all the software in the world is a
scary prospect, though compared to the amount of data we currently
keep for people it is a blip. And I'm not sure how else we can really
achieve the level of reproducibility we desire.
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Re: [galaxy-dev] tool_dependencies.xml format

[John Chilton]

James, et. al.

I think it is interesting that there was push back on providing
infrastructure (tool actions) for obtaining CBL from github and
performing installs based on it because it was not in the tool shed
and therefore less reproducible, but the team believes infrastructure
should be put in place to support pypi.

I understand there are any number of distinctions that could be made
here - perhaps you have made the calculation pypi is more stable than
github (either in terms or immutability or funding), perhaps the
setuptools mechanism is more general and could potentially support
grabbing these tar balls from the tool shed (or a tool shed adjacent
object store).

I think we all value reproduciblity here, but we make different
calculations on what is reproducible. I think in terms of implementing
the ideas James has laid out or similar things I have proposed, it
might be beneficial to have some final answers on what external
resources are allowed - both for obtaining a Galaxy IUC gold star and
for the tool shed providing infrastructure to support their usage.

I don't know if this takes for the form of the IUC voting or James
and/or Greg issuing a proclamation, but it would be good to get firm
answers on these two questions for the following sites rubygems, pypi,
github, bitbucket, cpan, cran, sourceforge, and google code. It would
also be great to have a process in place for deciding these questions
for future repositories.

Thanks,
-John

On Mon, Aug 26, 2013 at 9:05 AM, James Taylor  wrote:
> All,
>
> I've been seeing some examples of tool_depedencies.xml come across of
> the list, and I'm wondering if there are ways that it can be
> simplified. When we were first defining these features, we talked
> about having high level recipes for certain types of installs. This
> could greatly simplify things. For example, can this:
>
> 
> 
> 
> 
>  type="download_by_url">http://pypi.python.org/packages/source/r/requests/re
> quests-1.2.3.tar.gz
>  type="make_directory">$INSTALL_DIR/lib/python
> export
> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
> python setup.py install --home $INSTALL_DIR
> --install-scripts $INSTALL_DIR/bin
> 
>  action="append_to">$INSTALL_DIR/lib/python
>  action="prepend_to">$INSTALL_DIR/bin
> 
>
> 
> 
> 
> 
> 
> 
>
> Be simplified to:
>
> 
> 
> 
> url="http://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz";
> />
> 
>
> The assumptions are: when version is not provided, it is 1.0 (we've
> always maintained compatibility in the past for config files so
> hopefully this never changes), when installing a python package the
> install directories and environment variables that need to be set are
> always the same.
>
> Similar recipes could be:
>
> autoconf: default to configure; make; make install, allow providing
> configuration options
> make_install: just make; make install; allow providing make options
> python_virtualenv
> ruby_rbenv
> r_package
> ...
>
> Basically, most of the times the steps to install a particular package
> are boilerplate, this would remove a ton of duplication in the recipe
> files. Also, a likely less popular proposal would be to go one step
> further, tool_dependencies.yaml:
>
> recipe: python_package_setuptools
> name: requests
> version: 1.2.3
> url: 
> http://pypi.python.org/packages/source/r/requests/requests-${version}.tar.gz
>
> -- jt
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Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

[Peter Cock]

On Mon, Aug 26, 2013 at 3:10 PM, Dave Bouvier  wrote:
> Peter,
>
> I apologize for the delay, here is the information you requested:
>
> ubuntu@ip-10-0-0-243:~$ uname -a
> Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC
> 2013 x86_64 x86_64 x86_64 GNU/Linux
> ubuntu@ip-10-0-0-243:~$ arch
> x86_64
> ubuntu@ip-10-0-0-243:~$ echo $0
> -bash
>
>--Dave B.

Thanks Dave,

Sadly that looks just like my server where it works,

$ uname
Linux
$ arch
x86_64
$ echo $0
-bash

I was considering trying to have the tool_dependencies.xml install
recipe call a shell or Python script instead - but the new Tool Shed
"Tool dependency definition" repository type prevents that (unless
using a workaround like downloading the script first).

Hmm. Does anyone have any ideas on this error return code 64?

Regards,

Peter
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Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

[Dave Bouvier]

Peter,

I apologize for the delay, here is the information you requested:

ubuntu@ip-10-0-0-243:~$ uname -a
Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

ubuntu@ip-10-0-0-243:~$ arch
x86_64
ubuntu@ip-10-0-0-243:~$ echo $0
-bash

   --Dave B.

On 08/26/2013 09:44 AM, Peter Cock wrote:

(Off list)

Hi Dave, Greg,

Just a reminder - without a bit more information about the Tool Shed
cluster I am stuck about how to debug this install issue.

Thanks,

Peter


On Wed, Aug 21, 2013 at 2:05 PM, Peter Cock  wrote:

On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier  wrote:

Peter,

Here is the relevant log output for the installation of ncbi_blast_plus. A
quick google informs me that exit code 64 means "command line usage error",
for what it's worth.

...
tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new row
(or updating an existing row) for repository 'package_blast_plus_2_2_26' in
the tool_shed_repository table, status set to 'New'.

Warning: local() encountered an error (return code 64) while executing '
 if [[ "$(uname)" == "Linux" ]]; then export
FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi &&
 if [[ "$(arch)" == "x86_64" ]]; then export
FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi &&
 if [[ "$(uname)" == "Darwin" ]]; then export
FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi &&
 echo Fetching $FILENAME &&
 if [[ "$(uname)" == "Linux" ]]; then wget
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &&
 if [[ "$(uname)" == "Darwin" ]]; then curl -O
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &&
 tar -zxvf $FILENAME &&
 echo Downloaded and decompressed
 '



Thanks Dave,

I've made a note on this Trello card about exposing the log information
of unsuccessful builds on the Tool Shed,
https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages

Can you tell me what version of Linux this is, and which shell?

$ uname
...

$ arch
...

$ echo $0
...

That might give me a clue about the nature of the failure. My
hunch is that I am using something bash specific.

The simplest solution would be if you could run each of these
command by hand to see if it triggers the same error:

if [[ "$(uname)" == "Linux" ]]; then export 
FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi
if [[ "$(arch)" == "x86_64" ]]; then export 
FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi
if [[ "$(uname)" == "Darwin" ]]; then export 
FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi
echo Fetching $FILENAME
if [[ "$(uname)" == "Linux" ]]; then wget 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
if [[ "$(uname)" == "Darwin" ]]; then curl -O 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
tar -zxvf $FILENAME
echo Downloaded and decompressed

Thanks,

Peter

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[galaxy-dev] Manhattan/qq plots

[Berner, Thomas]

Hey guys,

we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1 
and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only 
pval qqplot.pdf is generated and we are getting the following error:

Nonzero exit code = 1
[1] "### 11008 values read from 
/opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read - now running 
plots"

'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in version 
0.9.1)

Setting the plot title with opts(title="...") is deprecated.

Use labs(title="...") or ggtitle("...") instead. (Deprecated; last used in 
version 0.9.1)

Scale for 'x' is already present. Adding another scale for 'x', which will 
replace the existing scale.

Scale for 'y' is already present. Adding another scale for 'y', which will 
replace the existing scale.

[1] "## qqplot on pval done"

[1] "## manhattan on pval starting 1 2 3"

Error in structure(list(call = match.call(), aesthetics = aesthetics,  :

  argument "values" is missing, with no default

Calls: rgqqMan ... scale_colour_manual -> manual_scale -> discrete_scale -> 
structure

Execution halted


At the galaxy-main ist working without any problems using the same input file.
All the necessary packages should be installed.

Any ideas? Thanks for your help.

Thomas
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[galaxy-dev] tool_dependencies.xml format

[James Taylor]

All,

I've been seeing some examples of tool_depedencies.xml come across of
the list, and I'm wondering if there are ways that it can be
simplified. When we were first defining these features, we talked
about having high level recipes for certain types of installs. This
could greatly simplify things. For example, can this:





http://pypi.python.org/packages/source/r/requests/re
quests-1.2.3.tar.gz
$INSTALL_DIR/lib/python
export
PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
python setup.py install --home $INSTALL_DIR
--install-scripts $INSTALL_DIR/bin

$INSTALL_DIR/lib/python
$INSTALL_DIR/bin









Be simplified to:



http://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz";
/>


The assumptions are: when version is not provided, it is 1.0 (we've
always maintained compatibility in the past for config files so
hopefully this never changes), when installing a python package the
install directories and environment variables that need to be set are
always the same.

Similar recipes could be:

autoconf: default to configure; make; make install, allow providing
configuration options
make_install: just make; make install; allow providing make options
python_virtualenv
ruby_rbenv
r_package
...

Basically, most of the times the steps to install a particular package
are boilerplate, this would remove a ton of duplication in the recipe
files. Also, a likely less popular proposal would be to go one step
further, tool_dependencies.yaml:

recipe: python_package_setuptools
name: requests
version: 1.2.3
url: 
http://pypi.python.org/packages/source/r/requests/requests-${version}.tar.gz

-- jt
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Re: [galaxy-dev] TS API installation broken

[Dave Bouvier]

Björn,

Thank you for the report, which revealed that there was another place 
where this error was occurring. It has been fixed in 10447:e97f613a4948, 
and that revision is now running on the test tool shed.


   --Dave B.

On 08/26/2013 08:38 AM, Dave Bouvier wrote:

Björn,

This looks like an issue that was fixed in 10444:ab74f2d80173, can you
confirm that you are running that revision or later locally?

--Dave B.

On 08/26/2013 07:46 AM, Bjoern Gruening wrote:

Hi,

if I try to install a repository via API I get the following error:

Traceback (most recent call last):
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py",
line 189, in decorator
 rval = func( self, trans, *args, **kwargs)
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
line 265, in install_repository_revision
 tool_shed_repository_dict =
tool_shed_repository.as_dict(
value_mapper=default_tool_shed_repository_value_mapper( trans,
tool_shed_repository ) )
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py",
line 3350, in as_dict
 return self.dictify( view='element', value_mapper=value_mapper )
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py",
line 3445, in dictify
 raise Exception( 'Unknown API view: %s' % view )
Exception: Unknown API view: element


Command line: python ./scripts/api/install_tool_shed_repositories.py
--api f1326e8588535c628f03a0df517e2247 -l http://localhost:8080 --url
http://toolshed.g2.bx.psu.edu/ -o devteam -r 4676e145a44e --name
add_value

Cheers,
Bjoern

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Re: [galaxy-dev] TS API installation broken

[Dave Bouvier]

Björn,

This looks like an issue that was fixed in 10444:ab74f2d80173, can you 
confirm that you are running that revision or later locally?


   --Dave B.

On 08/26/2013 07:46 AM, Bjoern Gruening wrote:

Hi,

if I try to install a repository via API I get the following error:

Traceback (most recent call last):
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py",
 line 189, in decorator
 rval = func( self, trans, *args, **kwargs)
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
 line 265, in install_repository_revision
 tool_shed_repository_dict =
tool_shed_repository.as_dict( 
value_mapper=default_tool_shed_repository_value_mapper( trans, 
tool_shed_repository ) )
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py", 
line 3350, in as_dict
 return self.dictify( view='element', value_mapper=value_mapper )
   File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py", 
line 3445, in dictify
 raise Exception( 'Unknown API view: %s' % view )
Exception: Unknown API view: element


Command line: python ./scripts/api/install_tool_shed_repositories.py
--api f1326e8588535c628f03a0df517e2247 -l http://localhost:8080 --url
http://toolshed.g2.bx.psu.edu/ -o devteam -r 4676e145a44e --name
add_value

Cheers,
Bjoern

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[galaxy-dev] TS API installation broken

[Bjoern Gruening]

Hi,

if I try to install a repository via API I get the following error:

Traceback (most recent call last):
  File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py",
 line 189, in decorator
rval = func( self, trans, *args, **kwargs)
  File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
 line 265, in install_repository_revision
tool_shed_repository_dict =
tool_shed_repository.as_dict( 
value_mapper=default_tool_shed_repository_value_mapper( trans, 
tool_shed_repository ) )
  File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py", 
line 3350, in as_dict
return self.dictify( view='element', value_mapper=value_mapper )
  File
"/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py", 
line 3445, in dictify
raise Exception( 'Unknown API view: %s' % view )
Exception: Unknown API view: element


Command line: python ./scripts/api/install_tool_shed_repositories.py
--api f1326e8588535c628f03a0df517e2247 -l http://localhost:8080 --url
http://toolshed.g2.bx.psu.edu/ -o devteam -r 4676e145a44e --name
add_value

Cheers,
Bjoern

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[galaxy-dev] tool not runing in workflow

[Berner, Thomas]

Hey guys,

we installed and used a tool of the mothur_toolsuite  in our local galaxy 
instance named "get.otulist", but if we want to integrate it into a workflow 
(extract from history) we get the following error for the next step:

"Error due to input mapping of 'Join two datasets' in 
'__new_primary_file_logfile|0.03.otu__'. A common cause of this is conditional 
outputs that cannot be determined until runtime, please review your workflow."

In the workflow editor only the *.html file is displayed as output but not the 
tabular file which is generated by the tool normally.
There should be an output (tabular) which we want to join with another one, but 
this doesn't work in the workflow.

Can somebody give me a hint for this?

Greetings, Thomas
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[galaxy-dev] Select multiple and conditional

[Kahlke Tim]

Hei,

Is it possible to use a  for a conditional? I'm trying 
to use it for checkboxes which by default have to have multiple set. But as 
soon as I put the multiple-tag in I get an 'no case matched' exception (see 
example below).

Any suggestions?
Tim


Example (working)


Blast
Fasta


...




Example (exception)


Blast
Fasta


...



=> Exception: ('No class matched value:' , 'c1' , None)

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[galaxy-dev] Postgresql database cleaning

[Christophe Antoniewski]

Hi everybody,

The python scripts to clean histories, datasets, users etc.. are fine...
However, the records are not really removed from the postgresql database
and as a result, this one gets bigger and bigger with unused records. Ours
is above 1 To after 2 years of production.

Is there a safe way to clean the database from unused records and their
dependencies to reduce it size, without being a postgresql guru ?

Chris
-- 

Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org
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