[galaxy-dev] Test Tool Shed down?

[Lionel Guy]

Good morning Galaxy,

It appears that the test tool shed is down, returning a 502 Bad Gateway 
message. The main tool shed is fine.

I'm not sure that this is the right place to announce that, but since I don't 
know who is in charge of the servers, I give it a shot...

Cheers,

Lionel
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Re: [galaxy-dev] Duplicated entries in "Manage installed tool shed repositories" table

[Peter Cock]

On Wed, Aug 14, 2013 at 11:08 PM, Ross  wrote:

> FWIW: I've managed to produce a few of these too - generally arose after
> futzing with a failed dependency, reaching for the "nuke it" ( 'completely
> remove' tool) button, then reinstalling it - sometimes there's a complaint
> that the same version was previously installed (even though it had been
> supposedly totally nuked), sometimes not - but occasionally a white 'new'
> ghost will reappear in the manage installed tools list after reinstallation
> - AFAIK those white ghosts are impossible to remove...
>
>
Thanks Ross,

It is good to know this isn't an isolated problem - and I too had been
"nuking" failed installs, starting with the July 2013 galaxy-dist but also
the August galaxy-dist. Maybe that will help Dave reproduce it?

I like your name "white ghost" for this since the "new" entry is shown on
with a white background (it didn't show up in the HTML email sadly).

Peter
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[galaxy-dev] Tool Shed error: AttributeError: 'NoneType' object has no attribute 'status'

[Bjoern Gruening]

Hi,

back for testing and migrating to the tool shed. Sorry in advance!

During installation via the API I'm usually watching the status with
'Manage installed tool shed repositories'. 
Installation is still running but I now get these error:

URL: http://localhost:8080/admin_toolshed/browse_repositories
File
'/home/gruening/projects/code/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
 line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File '/usr/lib/python2.7/site-packages/paste/recursive.py', line 84 in
__call__
  return self.application(environ, start_response)
File '/usr/lib/python2.7/site-packages/paste/httpexceptions.py', line
633 in __call__
  return self.application(environ, start_response)
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/base.py', 
line 132 in __call__
  return self.handle_request( environ, start_response )
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/base.py', 
line 190 in handle_request
  body = method( trans, **kwargs )
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py',
 line 221 in decorator
  return func( self, trans, *args, **kwargs )
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 151 in browse_repositories
  return self.installed_repository_grid( trans, **kwd )
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/helpers/grids.py',
 line 288 in __call__
  kwargs=kwargs )
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py',
 line 990 in fill_template
  return self.fill_template_mako( filename, **kwargs )
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py',
 line 1005 in fill_template_mako
  return template.render( **data )
File
'/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
 line 296 in render
  return runtime._render(self, self.callable_, args, data)
File
'/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
 line 660 in _render
  **_kwargs_for_callable(callable_, data))
File
'/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
 line 692 in _render_context
  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File
'/home/gruening/projects/code/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
 line 718 in _exec_template
  callable_(context, *args, **kwargs)
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/base.mako.py',
 line 42 in render_body
  __M_writer(unicode(next.body()))
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py',
 line 127 in render_body
  __M_writer(unicode(self.grid_body( grid )))
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py',
 line 747 in render_grid_body
  __M_writer(unicode(self.make_grid( grid )))
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py',
 line 777 in render_make_grid
  __M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes
)))
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py',
 line 724 in render_render_grid_table
  __M_writer(unicode(render_grid_table_body_contents( grid,
show_item_checkboxes )))
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py',
 line 627 in render_grid_table_body_contents
  return
render_render_grid_table_body_contents(context,grid,show_item_checkboxes)
File
'/home/gruening/projects/code/galaxy-central/database/compiled_templates/grid_base.mako.py',
 line 335 in render_render_grid_table_body_contents
  value = column.get_value( trans, grid, item )
File
'/home/gruening/projects/code/galaxy-central/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py',
 line 58 in get_value
  if tool_shed_repository.missing_repository_dependencies:
File
'/home/gruening/projects/code/galaxy-central/lib/galaxy/model/__init__.py', 
line 3566 in missing_repository_dependencies
  if required_repository.status not in
[ self.installation_status.INSTALLED ]:
AttributeError: 'NoneType' object has no attribute 'status'

Cheers,
Bjoern
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[galaxy-dev] Searching on Tool Shed gives multiple revisions

[Peter Cock]

Hi all,

Using the left hand menu items "Search for valid tools" and
"Search for workflows" gives multiple revisions - whereas
searching via the prominent search box on the welcome
page does not (only the latest revisions are shown).

I would prefer only to get the latest revision - otherwise the
search results are a bit confusing and the old revisions
are noise drowning out the main information.

Regards,

Peter
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[galaxy-dev] One installable revision is not working for orphan-tool-dependencies -> Was: Action type 'template_command' on galaxy-dist?

[Bjoern Gruening]

Hi Dave,

the bug is unfortunately still present in the latest Galaxy version.

If you try to install
http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end
up with an error, because numpy is not found. That error appears because
scipy was uploaded and afterwards numpy was changed. The consequence is
that scipy references on old (not installable) version of numpy and
crashes. 

I would expect that scipy is always looking for the latest version of
numpy regardless of what is specified in the numpy XML file. Is that
assumption wrong? That would raise the question if revisions are still
needed for orphan-tool-dependencies or 'Tool dependency definition'.

Is that bug easy to fix? Or do I need to upload all my repositories in
the right order again? That would be the consequence, because otherwise
I do not get the revision tag updated.

Thanks!
Bjoern


> Peter, Björn,
> 
> The August Galaxy release is out, and the template_command is now in the 
> stable repository and branch. Regarding matplotlib and numpy, I 
> currently only see matplotlib depending on the 74c21f9bdc39 revision of 
> numpy. Is this still an issue, or has it been resolved?
> 
> --Dave B.
> 
> On 8/12/13 11:36:00.000, Bjoern Gruening wrote:
> > On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
> >> On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
> >>  wrote:
> >>> On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
>  Maybe I should retitle this thread...
> 
>  On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock  
>  wrote:
> >
> > Thank you - installing the NumPy package now works for me,
> > http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
> >
> > I'm moving on to something odd with matplotlib instead...
> >
> > Peter
> 
>  There are currently two revisions to the main Tool Shed
>  package for numpy,
>  http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
> 
>  Rev 0: c75482be1d3a - needs not-yet-released features
>  Rev 1: 74c21f9bdc39 - simplified
> 
>  I'm trying to install a package dependent on this via
>  matplotlib - but installing the matplotlib package fails:
>  http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2
> 
>  This is something odd, why does it think it needs to install
>  the rev 0 c75482be1d3a version of package_numpy_1_7?
>  See screenshot, except here:
> 
>  Repository dependencies - installation of these additional
>  repositories is required
>  Name  RevisionOwner   Installation status
>  package_freetype_2_4  8761091302c4iuc Installed
>  package_numpy_1_7 74c21f9bdc39iuc Installed
>  package_numpy_1_7 c75482be1d3aiuc Uninstalled
> 
>  Yes, the matplotlib tool_dependencies.xml does list the
>  original revision:
> 
>   
>    name="package_numpy_1_7" owner="iuc"
>  prior_installation_required="True"
>  toolshed="http://toolshed.g2.bx.psu.edu"; />
>   
>   
>     name="package_freetype_2_4" owner="iuc"
>  prior_installation_required="True"
>  toolshed="http://toolshed.g2.bx.psu.edu"; />
>   
> 
>  But I thought as a "Tool dependency definition" only the
>  tip revision is ever used?
> >>>
> >>> That is also what I understood, regardless of the revision there is only
> >>> one install able revision. But I guess the TS is generating the path to
> >>> numpy from the  tag and that points to an old non existing
> >>> version.
> >>
> >> Hmm. Something for Greg to look at then.
> >>
>  After attempting to install this, the status is "Installed, missing
>  repository dependencies" and this oddity about wanting two
>  revisions of NumPy persists.
> 
>  The actual failure appears to be in compiling matplotlib itself...
>  I don't think it is finding the NumPy installation.
> 
>  Is it possible to view the INSTALLATION.log from within the
>  Galaxy Admin web interface?
> >>>
> >>> Yes you should see all installed files/folder and the INSTALLATION.log
> >>> in your web browser.
> >>
> >> Can you give me a little more information on how to see
> >> this from within Galaxy?
> >>
> >> 1. Open my Galaxy instance and log in,
> >> 2. Click on "Admin" from top menu
> >> 3. Click on "Manage installed tool shed repositories" on left
> >> 4. Select repository of interest
> >
> > 5. Click, "Manage tool dependencies"
> > 6. Choose one of the dependencies
> >
> > There should be a tree like structure to navigate to your
> > INSTALLATION.log file besides your env.sh file.
> >
> >> At this point the repository drop down menus I see are
> >> "Get updates" and "Delete or inactivate". I must be looking
> >> in the wrong place?
> >>
> >>>
> >>> I can reproduce it here and it fails because of numpy.
> >>
> >> OK, that's good - it sounds like the rival revision problem
> >> is what is going wrong.
> >>

Re: [galaxy-dev] Test Tool Shed down?

[Dave Bouvier]

Lionel,

Thank you for reporting this, the test tool shed is now running again.

   --Dave B.

On 8/15/13 03:48:14.000, Lionel Guy wrote:

Good morning Galaxy,

It appears that the test tool shed is down, returning a 502 Bad Gateway 
message. The main tool shed is fine.

I'm not sure that this is the right place to announce that, but since I don't 
know who is in charge of the servers, I give it a shot...

Cheers,

Lionel
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Re: [galaxy-dev] Test Tool Shed down?

[Peter Cock]

On Thu, Aug 15, 2013 at 2:09 PM, Dave Bouvier  wrote:
> Lionel,
>
> Thank you for reporting this, the test tool shed is now running again.
>
>--Dave B.

Thanks Dave - did the overnight tests get run as usual or might
some have been interrupted?

Peter
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Re: [galaxy-dev] Test Tool Shed down?

[Dave Bouvier]

Peter,

Thanks for the reminder, they did indeed not run. I'm running them 
manually, and you should see updated results within a few hours.


   --Dave B.

On 8/15/13 09:19:50.000, Peter Cock wrote:

On Thu, Aug 15, 2013 at 2:09 PM, Dave Bouvier  wrote:

Lionel,

Thank you for reporting this, the test tool shed is now running again.

--Dave B.


Thanks Dave - did the overnight tests get run as usual or might
some have been interrupted?

Peter


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Re: [galaxy-dev] Test Tool Shed down?

[Peter Cock]

On Thu, Aug 15, 2013 at 2:24 PM, Dave Bouvier  wrote:
> Peter,
>
> Thanks for the reminder, they did indeed not run. I'm running them manually,
> and you should see updated results within a few hours.
>
>--Dave B.

Lovely, cheers :)

Peter
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Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies -> Was: Action type 'template_command' on galaxy-dist?

[Dave Bouvier]

Peter,

I've duplicated the installation error on the scipy tool dependency, and 
will be looking into the cause. Thanks for the report.


   --Dave B.

On 8/15/13 09:01:17.000, Bjoern Gruening wrote:

Hi Dave,

the bug is unfortunately still present in the latest Galaxy version.

If you try to install
http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end
up with an error, because numpy is not found. That error appears because
scipy was uploaded and afterwards numpy was changed. The consequence is
that scipy references on old (not installable) version of numpy and
crashes.

I would expect that scipy is always looking for the latest version of
numpy regardless of what is specified in the numpy XML file. Is that
assumption wrong? That would raise the question if revisions are still
needed for orphan-tool-dependencies or 'Tool dependency definition'.

Is that bug easy to fix? Or do I need to upload all my repositories in
the right order again? That would be the consequence, because otherwise
I do not get the revision tag updated.

Thanks!
Bjoern



Peter, Björn,

The August Galaxy release is out, and the template_command is now in the
stable repository and branch. Regarding matplotlib and numpy, I
currently only see matplotlib depending on the 74c21f9bdc39 revision of
numpy. Is this still an issue, or has it been resolved?

 --Dave B.

On 8/12/13 11:36:00.000, Bjoern Gruening wrote:

On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:

On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
 wrote:

On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:

Maybe I should retitle this thread...

On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock  wrote:


Thank you - installing the NumPy package now works for me,
http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7

I'm moving on to something odd with matplotlib instead...

Peter


There are currently two revisions to the main Tool Shed
package for numpy,
http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7

Rev 0: c75482be1d3a - needs not-yet-released features
Rev 1: 74c21f9bdc39 - simplified

I'm trying to install a package dependent on this via
matplotlib - but installing the matplotlib package fails:
http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2

This is something odd, why does it think it needs to install
the rev 0 c75482be1d3a version of package_numpy_1_7?
See screenshot, except here:

Repository dependencies - installation of these additional
repositories is required
Name  RevisionOwner   Installation status
package_freetype_2_4  8761091302c4iuc Installed
package_numpy_1_7 74c21f9bdc39iuc Installed
package_numpy_1_7 c75482be1d3aiuc Uninstalled

Yes, the matplotlib tool_dependencies.xml does list the
original revision:

  
 http://toolshed.g2.bx.psu.edu"; />
  
  
  http://toolshed.g2.bx.psu.edu"; />
  

But I thought as a "Tool dependency definition" only the
tip revision is ever used?


That is also what I understood, regardless of the revision there is only
one install able revision. But I guess the TS is generating the path to
numpy from the  tag and that points to an old non existing
version.


Hmm. Something for Greg to look at then.


After attempting to install this, the status is "Installed, missing
repository dependencies" and this oddity about wanting two
revisions of NumPy persists.

The actual failure appears to be in compiling matplotlib itself...
I don't think it is finding the NumPy installation.

Is it possible to view the INSTALLATION.log from within the
Galaxy Admin web interface?


Yes you should see all installed files/folder and the INSTALLATION.log
in your web browser.


Can you give me a little more information on how to see
this from within Galaxy?

1. Open my Galaxy instance and log in,
2. Click on "Admin" from top menu
3. Click on "Manage installed tool shed repositories" on left
4. Select repository of interest


5. Click, "Manage tool dependencies"
6. Choose one of the dependencies

There should be a tree like structure to navigate to your
INSTALLATION.log file besides your env.sh file.


At this point the repository drop down menus I see are
"Get updates" and "Delete or inactivate". I must be looking
in the wrong place?



I can reproduce it here and it fails because of numpy.


OK, that's good - it sounds like the rival revision problem
is what is going wrong.



One fix to get it working is to upload again biopython.


Good plan - as discussed here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016001.html


Done.


Thank you,

Peter



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Re: [galaxy-dev] Searching on Tool Shed gives multiple revisions

[Dave Bouvier]

Peter,

Judging by the code, the "search for valid tools" page is intended to 
search with greater granularity for valid tool versions, and displays 
every tool found with a unique version, whereas the prominent search 
page is intended as a general search for repository names matching the 
given query.


   --Dave B.

On 8/15/13 06:08:58.000, Peter Cock wrote:

Hi all,

Using the left hand menu items "Search for valid tools" and
"Search for workflows" gives multiple revisions - whereas
searching via the prominent search box on the welcome
page does not (only the latest revisions are shown).

I would prefer only to get the latest revision - otherwise the
search results are a bit confusing and the old revisions
are noise drowning out the main information.

Regards,

Peter
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Re: [galaxy-dev] Searching on Tool Shed gives multiple revisions

[Peter Cock]

On Thu, Aug 15, 2013 at 3:00 PM, Dave Bouvier  wrote:
> Peter,
>
> Judging by the code, the "search for valid tools" page is intended to search
> with greater granularity for valid tool versions, and displays every tool
> found with a unique version, whereas the prominent search page is intended
> as a general search for repository names matching the given query.
>
>--Dave B.

I was particularly interested in the "Search for workflows" option -
which can be used with a blank search term to get all repositories
with a workflow.

Is there a better way to get a (latest revision only) listing like that?

Thanks,

Peter
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Re: [galaxy-dev] Display data in browser

[Carl Eberhard]

Hello, Gromobir

First, I believe you'll need to make the following change in your
universe_wsgi.ini file:
sanitize_all_html = False

This will let galaxy treat html as valid output data.

For examples of tools that produce and show html, you might want to start
by looking at the xml and py files of some of Ross Lazarus' RGenetics tools:
tools/rgenetics/rgQC.xml, tools/rgenetics/rgFastQC.xml

Hope this helps,
Carl


On Mon, Jul 15, 2013 at 5:48 AM, Gromobir  wrote:

> Hello list,
> I'm currently trying to create a new tool, which has an .xhtml file as its
> output.
> After finishing the job, I would like to be able to click on the "eye
> icon" aka "Display data in browser"
> and display the resulting .xhtml file in the frame to the left of my tool
> history. Unfortunately I have no idea yet
> how I could accomplish this. Any help is highly appreciated.
>
> Best regards,
> Gromobir
> __**_
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> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
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>  
> http://galaxyproject.org/**search/mailinglists/
>
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Re: [galaxy-dev] how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini

[Nate Coraor]

On Aug 14, 2013, at 9:46 PM, tin h wrote:

> 
> Hello gurus, 
> 
> 
> I made some slight progress...
> 
> If I specify a handlers section into the job_conf.xml file with:
> 
> 
> 
> 
> 
> Then galaxy would at least start.  However, it is not very functional, I 
> can't upload files or run job, it says:
> 
> An error occurred with this dataset:Unable to run job due to a 
> misconfiguration of the Galaxy job running system. Please contact a site 
> administrator.
> 
> 
> My universe_wsgi.conf is fairly stock, the [server:main] section is certainly 
> there.  The most relevant changes are:
> start_job_runners = drmaa
> default_cluster_job_runner =  drmaa://-q default.q -V -v TMPDIR=/scratch/
> 
> 
> If someone can point me to a job_conf.xml so that I can set the TMPDIR param 
> correctly for qsub (sge), that would be greatly appreciated!
> 
> Thanks
> -Tin

Hi Tin,

The start_job_runners and default_cluster_job_runner parameters are ignored 
once you switch to the new XML configuration.  The problem is most likely that 
the 'runner' attribute on your destination ("drmaa") does not match the 'id' 
attribute of the DRMAAJobRunner plugin ("sge"), so try changing one or the 
other so that they match.  More details regarding the error should be shown in 
the log.

--nate

> 
> 
> 
> 
> On Wed, Aug 14, 2013 at 8:04 AM, Jennifer Jackson  wrote:
>  Original Message 
> Subject:  Re: how to add settings of TMPDIR=/scratch for sge/drmaa in 
> universe_wsgi.ini
> Date: Tue, 13 Aug 2013 23:21:16 -0700
> From: tin h 
> To:   Jennifer Jackson 
> CC:   Galaxy Dev 
> 
> 
> 
> Thank you Jennifer.
> 
> I am not sure if my previous email got gabled up...
> Just to be sure, I specified the following in universe_wsgi.ini
>  default_cluster_job_runner = drmaa://-q default.q -V -v TMPDIR=/scratch/ 
> 
> when i start galaxy, looking at the console log, this is what I see:
> 
> 
> galaxy.jobs DEBUG 2013-08-14 14:08:14,885 Loaded job runner 
> 'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa'
> galaxy.jobs.runners.drmaa DEBUG 2013-08-14 14:08:14,885 Converted URL 
> 'drmaa://-q default.q -V -v TMPDIR=/scratch/' to destination runner=drmaa, 
> params={'nativeSpecification': '-q default.q -V -v TMPDIR='}
> galaxy.jobs DEBUG 2013-08-14 14:08:14,885 Legacy destination with id 
> 'drmaa://-q default.q -V -v TMPDIR=/scratch/', url 'drmaa://-q default.q -V 
> -v TMPDIR=/scratch/' converted, got params:
> galaxy.jobs DEBUG 2013-08-14 14:08:14,885 nativeSpecification: -q 
> default.q -V -v TMPDIR=
> 
> 
> The parser has stopped at the / before scratch and ignored the rest :(
> 
> 
> I did  refer to 
> http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster and tried to 
> define job_conf.xml as
> 
> 
> 
> 
>  load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> 
>  load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
> 
> 
> 
> -q default.q -V -v 
> TMPDIR=/scratch
> 
> 
> 
> 
> 
> But then galaxy won't start, giving me the error of:
> 
> Traceback (most recent call last):
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", 
> line 37, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 95, in __init__
> self.job_config = jobs.JobConfiguration(self)
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 107, 
> in __init__
> self.__parse_job_conf_xml(tree)
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 157, 
> in __parse_job_conf_xml
> self.default_handler_id = self.__get_default(handlers, 
> self.handlers.keys())
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 286, 
> in __get_default
> rval = parent.get('default')
> AttributeError: 'NoneType' object has no attribute 'get'
> 
> I am not sure what the "default" refers to, doesn't seems to be the 
> destinations default specified as I tried changing that name but the error 
> message remains the same.
> 
> Any help so that I can pass TMPDIR=/scratch into SGE qsub would be greatly 
> appreciated.
> 
> 
> -Tin
> 
> 
> 
> 
> --
> 
> I am riding to fundraise for the Cystic Fibrosis Foundation.  Please consider 
> a tax deductible donation at 
> http://www.cff.org/LWC/dsp_DonationPage.cfm?idEvent=23815&idUser=615989
> 
> 
> ~~~__oEngineering is the art of making 
> compromises.
>  ~~~ _ <_ Science is the reverse engineering of 
> the compromises made by nature.
>~~~  (_)/(_)Medicine is the hacking of the 
> scientific knowledge base.   - A comp sci student :-)
> 
> On 8/13/13 7:28 PM, Jennifer Jackson wrote:
>> Hi Tin,
>> 
>> I am going to move this over to the galaxy-...@bx.psu.edu mailing list (good 
>> for local install questions) to give it better viabili

Re: [galaxy-dev] Job listing exception

[Carl Eberhard]

That's a great point. I've made a bug card for it here:
https://trello.com/c/LsZoPtwv/1053-jobs-better-unicode-handling-in-stderr

Thanks for reporting this.
Carl


On Sat, Jul 6, 2013 at 11:33 PM, Kyle Ellrott  wrote:

> This also took out my job handlers (exception below). So the introduction
> of non-ascii characters into the table (via the job stdout/stderr capture)
> can make a galaxy instance pretty useless.
>
> I was able to find the offending records using "SELECT count(*) FROM job
> WHERE stderr similar to '%\x8b%';"
> Turns out it was the byproduct of doing a path paste of some gzipped fastq
> files (so they where never decompressed, just passed along), and then
> fastq_groomer.py complains about the file having an invalid header (line
> 22?) reports back an invalid header and prints it out, thus the non-ascii
> characters in the stderr.
>
> I 'cleaned' the database with 'update job set stderr =
> regexp_replace(stderr, '\x8b', '\x5f');'. But there should probably be some
> safe guards put in place to stop this from happening.
>
> Kyle
>
>
>
> galaxy.jobs.handler INFO 2013-07-06 12:35:32,033 job handler stop queue
> started
> Traceback (most recent call last):
>   File "/inside/depot4/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
> 35, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/inside/depot4/galaxy/lib/galaxy/app.py", line 164, in __init__
> self.job_manager = manager.JobManager( self )
>   File "/inside/depot4/galaxy/lib/galaxy/jobs/manager.py", line 36, in
> __init__
> self.job_handler.start()
>   File "/inside/depot4/galaxy/lib/galaxy/jobs/handler.py", line 34, in
> start
> self.job_queue.start()
>   File "/inside/depot4/galaxy/lib/galaxy/jobs/handler.py", line 77, in
> start
> self.__check_jobs_at_startup()
>   File "/inside/depot4/galaxy/lib/galaxy/jobs/handler.py", line 92, in
> __check_jobs_at_startup
> & ( model.Job.handler == self.app.config.server_name ) ):
>   File
> "/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py",
> line 2341, in instances
> fetch = cursor.fetchall()
>   File
> "/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
> line 3204, in fetchall
> l = self.process_rows(self._fetchall_impl())
>   File
> "/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
> line 3171, in _fetchall_impl
> return self.cursor.fetchall()
> UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 404:
> ordinal not in range(128)
>
>
>
> On Fri, Jul 5, 2013 at 11:43 PM, Kyle Ellrott wrote:
>
>> I'm getting an exception when trying to look at the admin job management
>> screen. It looks like SQLAlchemy doesn't like non-ascii characters. Any
>> ideas about what to do?
>>
>>
>> Error - : 'ascii' codec can't
>> decode byte 0x8b in position 404: ordinal not in range(128)
>> URL: http://pk.kilokluster.ucsc.edu:8079/admin/jobs
>> File
>> '/inside/depot4/galaxy/lib/galaxy/web/framework/middleware/error.py', line
>> 149 in __call__
>>   app_iter = self.application(environ, sr_checker)
>> File
>> '/inside/depot4/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>> line 84 in __call__
>>   return self.application(environ, start_response)
>> File
>> '/inside/depot4/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>> line 633 in __call__
>>   return self.application(environ, start_response)
>> File '/inside/depot4/galaxy/lib/galaxy/web/framework/base.py', line 132
>> in __call__
>>   return self.handle_request( environ, start_response )
>> File '/inside/depot4/galaxy/lib/galaxy/web/framework/base.py', line 190
>> in handle_request
>>   body = method( trans, **kwargs )
>> File '/inside/depot4/galaxy/lib/galaxy/web/framework/__init__.py', line
>> 221 in decorator
>>   return func( self, trans, *args, **kwargs )
>> File '/inside/depot4/galaxy/lib/galaxy/web/base/controllers/admin.py',
>> line 1053 in jobs
>>   for job in jobs:
>> File
>> '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py',
>> line 2341 in instances
>> File
>> '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py',
>> line 3204 in fetchall
>> File
>> '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py',
>> line 3171 in _fetchall_impl
>> UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 404:
>> ordinal not in range(128)
>>
>>
>
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> in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Multiple output files do not appear in history

[Carl Eberhard]

Hello, Cristopher

Thanks for noticing this. I've updated the wiki entry:
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run

Does the line starting with 'Alternately,' match the behavior you're seeing?

Thanks,
Carl


On Wed, Jul 3, 2013 at 8:59 AM, Christoph Malisi <
christoph.mal...@computomics.com> wrote:

> Hi,
>
> I found my problem:
> in the production instances universe_wsgi.ini
> the value for "collect_outputs_from" was different that in my VM.
> It is set to:
> collect_outputs_from = job_working_directory
>
> Perhaps one could update the documentation that deals with multiple output
> files and mention that the $__new_file_path__ variable is not necessary, it
> is sufficient to name the output files correctly (i.e.
> primary_123_output2_visible_fastq,…) in the job work dir.
>
> Best,
> Chris
>
> universe_wsgi.ini
> On Jul 3, 2013, at 10:36 AM, Christoph Malisi <
> christoph.mal...@computomics.com> wrote:
>
> > Hey,
> >
> > I'm writing a XML for a tool that produces a number of output files. As
> the number is not known before the tool is run, I used the strategy
> outlined here:
> >
> http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
> >
> > First, I tried my tool definition in a galaxy instance in a virtual
> machine to not interrupt our production instance (we have a local instance
> set up). Here, everything worked fine. When trying the same code in our
> production galaxy instance, it didn't: Regardless of how many output files
> were produced, only one appears in the history. (the first one,
> corresponding to "output1" in the references wiki entry). When looking at
> the temp directory provided to the tool by galaxy ("$__new_file_dir__" in
> the wiki, it always points to "galaxy-dist/database/tmp/"), the additional
> output files have been created by my tool and are named correctly (e.g.
> primary_123_output2_visible_fastq, primary_123_output3_visible_fastq, …)
> >
> > Both instances are new, based on release_2013.06.03.
> >
> > Is there any setting in galaxy somewhere that could prevent this from
> working?
> >
> > Thanks for your help
> > Chris
> >
> > PS: I wrote a little python script that just creates multiple output
> files, and the discrepancy between the two instances is reproducible. Here
> is the code for the python script and the corresponding XML:
> >
> > ###
> > import subprocess
> > import argparse
> > import os
> >
> > def main():
> >   parser = argparse.ArgumentParser()
> >
> >   parser.add_argument('-i', type=int)
> >
> >   parser.add_argument('output1')
> >   parser.add_argument('output1_id')
> >   parser.add_argument('out_dir')
> >   args = parser.parse_args()
> >   print 'Wrapper arguments:', args
> >
> >   with open(args.output1, 'w') as f:
> >   f.write('output1')
> >
> >   for i in range(2, args.i+1):
> >   name = 'output%i'%i
> >   file_type = 'text'
> >   fname = '%s_%s_%s_%s_%s' % ('primary', args.output1_id, name,
> 'visible', file_type)
> >   with open(os.path.join(args.out_dir, fname), 'w') as f:
> >   f.write('output%i'%i)
> >
> > if __name__ == "__main__":
> >   main()
> > 
> > ###
> > 
> > Multiple Outputs test
> >   
> >   multiout.py
> >   -i $how_many
> >   $output1
> >   $output1.id
> >   $__new_file_path__
> >   
> > 
> > 
> > 
> > 
> >   
> > 
> > 
> > This is some help text.
> > 
> > 
> > #
> >
>
>
> ___
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[galaxy-dev] GATK - Depth of Coverage Error

[Can Holyavkin]

Hi Everyone,

Recently, I tried to use GATK - Depth of Coverage tool with my own .bam file on 
Galaxy for the first time. However it gave following error for each output. 
(see screenshot)

> Depth of Coverage on data 4 and data 1 (output cumulative coverage 
> proportions sample)
> error:
> An error occurred with this dataset: /bin/sh: 1: samtools: not found 
> Traceback (most recent call last): File 
> "/home/can/galaxy-dist/tools/gatk/gatk_wrapper.py", line 126, in if 
> __name__=="__main__": __main__() File 
> "/home/can/galaxy-dist/tools/gatk/gatk_wrapper.py", line 9


I searched the mailing list, but I couldn't find similar problem that posted 
before.

How can I solve it? Should I install GATK seperately on Galaxy? or anything 
else?

Can Holyavkin
PhD Student
Istanbul Technical University
Molecular Biology and Genetics Dept.___
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[galaxy-dev] Stopping jobs by deleting history via API

[Sytchev, Ilya]

Hi,

I was wondering if there are any near term plans to fix this issue?
https://trello.com/c/Tbota8xG/992-deleting-history-using-the-api-does-not-d
elete-stop-jobs 


Thanks,
Ilya


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[galaxy-dev] Error resolving Emboss tool dependencies

[Shantanu Pavgi (Campus)]

I have migrated Emboss tool from dist to tool-shed using the migration script 
and later updated it's revision. The tool was installed along with it's 
dependencies, but it's failing to find them during job run. It's logging 
following  'Failed to resolve dependency on 'emboss', ignoring' warning message 
in the log file. It seems like build_dependency_shell_commands method in 
'/lib/galaxy/tools/__init__.py' is unable to get installed_tool_dependencies. I 
am not sure why this would fail and how to resolve it. I have tried resetting 
tool metadata several times, but that didn't help. Appreciate any help on 
resolving this error. I am using Galaxy release_2013.06.03 revision.

Thanks,
Shantanu
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Re: [galaxy-dev] Error resolving Emboss tool dependencies

[Björn Grüning]

Hi Shantanu,

can you have a look in the Admin menu if EMBOSS is installed correctly
(green) or if it failed (red)?

Thanks,
Bjoern

> I have migrated Emboss tool from dist to tool-shed using the migration script 
> and later updated it's revision. The tool was installed along with it's 
> dependencies, but it's failing to find them during job run. It's logging 
> following  'Failed to resolve dependency on 'emboss', ignoring' warning 
> message in the log file. It seems like build_dependency_shell_commands method 
> in '/lib/galaxy/tools/__init__.py' is unable to get 
> installed_tool_dependencies. I am not sure why this would fail and how to 
> resolve it. I have tried resetting tool metadata several times, but that 
> didn't help. Appreciate any help on resolving this error. I am using Galaxy 
> release_2013.06.03 revision.
> 
> Thanks,
> Shantanu
> ___
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Re: [galaxy-dev] Error resolving Emboss tool dependencies

[Shantanu Pavgi (Campus)]

Thanks for the reply Bjoern. It's installed correctly - green box. The emboss 
entries in tool_dependency and tool_shed_repository look fine as well. If I 
directly run an emboss command (e.g. antigenic) from CLI then it seems to be 
working.

--
Shantanu

On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote:

> Hi Shantanu,
> 
> can you have a look in the Admin menu if EMBOSS is installed correctly
> (green) or if it failed (red)?
> 
> Thanks,
> Bjoern
> 
>> I have migrated Emboss tool from dist to tool-shed using the migration 
>> script and later updated it's revision. The tool was installed along with 
>> it's dependencies, but it's failing to find them during job run. It's 
>> logging following  'Failed to resolve dependency on 'emboss', ignoring' 
>> warning message in the log file. It seems like 
>> build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is 
>> unable to get installed_tool_dependencies. I am not sure why this would fail 
>> and how to resolve it. I have tried resetting tool metadata several times, 
>> but that didn't help. Appreciate any help on resolving this error. I am 
>> using Galaxy release_2013.06.03 revision.
>> 
>> Thanks,
>> Shantanu
>> ___
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>> and other Galaxy lists, please use the interface at:
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>> 
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>>  http://galaxyproject.org/search/mailinglists/
> 
> 
> 


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Re: [galaxy-dev] Error resolving Emboss tool dependencies

[Björn Grüning]

Hi,

> Thanks for the reply Bjoern. It's installed correctly - green box. The emboss 
> entries in tool_dependency and tool_shed_repository look fine as well. 
> If I directly run an emboss command (e.g. antigenic) from CLI then it seems 
> to be working.

can you check a few things or paste the complete warning message from
Failed to resolve dependency on 'emboss'?

- Do you have more than one EMBOSS suite installed or showing up in your
Tool Panel?
- Which version is shown if you run some EMBOSS tools?
- I assume tool shed, or test tool shed?
- can you give us the revision number of EMBOSS that is installed?

Thanks,
Bjoern

> --
> Shantanu
> 
> On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote:
> 
> > Hi Shantanu,
> > 
> > can you have a look in the Admin menu if EMBOSS is installed correctly
> > (green) or if it failed (red)?
> > 
> > Thanks,
> > Bjoern
> > 
> >> I have migrated Emboss tool from dist to tool-shed using the migration 
> >> script and later updated it's revision. The tool was installed along with 
> >> it's dependencies, but it's failing to find them during job run. 
> It's logging following  'Failed to resolve dependency on 'emboss', ignoring' 
> warning message in the log file. It seems like 
> build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is 
> unable to get installed_tool_dependencies. I am not sure why this would fail 
> and how to resolve it. I have tried resetting tool metadata several times, 
> but that didn't help. Appreciate any help on resolving this error. I am using 
> Galaxy release_2013.06.03 revision.
> >> 
> >> Thanks,
> >> Shantanu
> >> ___
> >> 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] Error resolving Emboss tool dependencies

[Shantanu Pavgi (Campus)]

There is only one EMBOSS suite in the tool panel. The EMBOSS tool repo is at 
revision c159a6ded912 and shows version 5.0.0 in the job panel. The tool was 
migrated using galaxy-dist provided migration script and later upgraded using 
the admin panel interface. The job fails with 'command not found error' which 
is resulting from 'Failed to build dependencies'.

Log entries:
{{{
galaxy.tools DEBUG 2013-08-15 15:25:16,021 Building dependency shell command 
for dependency 'emboss'
galaxy.tools.deps WARNING 2013-08-15 15:25:16,022  Base Path 
['/share/apps/galaxy/galaxydevelopstaging-tools']
galaxy.tools WARNING 2013-08-15 15:25:16,024 * calling 
self.app.toolbox.dependency_manager.find_dep with args emboss 5.0.0 package None

}}}

Line containing asterisk were added by me during debugging.

--
Thanks,
Shantanu


On Aug 15, 2013, at 3:10 PM, Björn Grüning wrote:

> Hi,
> 
>> Thanks for the reply Bjoern. It's installed correctly - green box. The 
>> emboss entries in tool_dependency and tool_shed_repository look fine as 
>> well. 
>> If I directly run an emboss command (e.g. antigenic) from CLI then it seems 
>> to be working.
> 
> can you check a few things or paste the complete warning message from
> Failed to resolve dependency on 'emboss'?
> 
> - Do you have more than one EMBOSS suite installed or showing up in your
> Tool Panel?
> - Which version is shown if you run some EMBOSS tools?
> - I assume tool shed, or test tool shed?
> - can you give us the revision number of EMBOSS that is installed?
> 
> Thanks,
> Bjoern
> 
>> --
>> Shantanu
>> 
>> On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote:
>> 
>>> Hi Shantanu,
>>> 
>>> can you have a look in the Admin menu if EMBOSS is installed correctly
>>> (green) or if it failed (red)?
>>> 
>>> Thanks,
>>> Bjoern
>>> 
 I have migrated Emboss tool from dist to tool-shed using the migration 
 script and later updated it's revision. The tool was installed along with 
 it's dependencies, but it's failing to find them during job run. 
>> It's logging following  'Failed to resolve dependency on 'emboss', ignoring' 
>> warning message in the log file. It seems like 
>> build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is 
>> unable to get installed_tool_dependencies. I am not sure why this would fail 
>> and how to resolve it. I have tried resetting tool metadata several times, 
>> but that didn't help. Appreciate any help on resolving this error. I am 
>> using Galaxy release_2013.06.03 revision.
 
 Thanks,
 Shantanu
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[galaxy-dev] Getting data from a database to create a dynamic combo box

[Ramon Tiburski]

Hi,
I need to create a combo box that will take data from a database dynamically. 
How could I do this?

Thank you
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Re: [galaxy-dev] Getting data from a database to create a dynamic combo box

[Björn Grüning]

Hi Ramon,

depends a little bit on what you mean with 'dynamically'.
I have some wrappers that may be interesting for you:

https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/pgchem/pgchem

Basically, you can choose the Database/Scheme dynamically and the SQL
query is also constructed dynamically. 

Cheers,
Bjoern 

> Hi,
> I need to create a combo box that will take data from a database
> dynamically. How could I do this?
> 
> Thank you
> 
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> and other Galaxy lists, please use the interface at:
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> 
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