galaxy-dev August 2013

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116 participants
210 discussions

Samtools 0.1.19 upgrade
by Björn Grüning 19 Aug '13

19 Aug '13

Hi devteam and and IUC Commissioners, I have uploaded an upgrade to the samtools package (0.1.19) to the test-tool shed. Main features are multi threading support for a few applications and bug fixes. Is anyone from the devteam interested in taking that over and migrating it to the devteam tool shed account? Or should it be an IUC package? Currently, it lives under the IUC account. Thanks, Bjoern

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error checking active jobs : KeyError: 'destination'
by Geert Vandeweyer 19 Aug '13

19 Aug '13

Hi, I'm getting errors in the handler logs after upgrading galaxy stable to today's release. I specified the "dynamic" job runner as default, which returns a job for pbs. These errors appear as soon as the server is up and running. What could be the issue here? galaxy.jobs.runners ERROR 2013-04-02 17:24:23,411 Unhandled exception checking active jobs Traceback (most recent call last): File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 336, in monitor self.check_watched_items() File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 382, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 463, in check_all_jobs pbs_server_name = self.__get_pbs_server(pbs_job_state.job_destination.params) File "/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 221, in __get_pbs_server return job_destination_params['destination'].split('@')[-1] KeyError: 'destination' -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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Picard Paired Read Mate Fixer Error with picard_wrapper.py
by Nicolas Quizon 17 Aug '13

17 Aug '13

Hi! I'm a student and newcomer to Galaxy. When I try to run the Picard Paired Read Mate Fixer on my local Galaxy the following error arises: File "/usr/lib/galaxy-server/tools/picard/picard_wrapper.py", line 173 runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir) ^ IndentationError: unexpected indent I've looked in the code, but the indentations seem to be correct? I have attached a copy of python_wrapper.py Thanks for any help you can provide!

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tool shed differences local vs web
by Benjamin Schuster-Boeckler 16 Aug '13

16 Aug '13

Yesterday, I noticed that there are some packages in http://toolshed.g2.bx.psu.edu that I can't find when I search the main tool shed on my local instance. I would have thought that the "Search and browse tool sheds" options under "Admin" is just a front-end for the search on the main tool shed on the web, so I was surprised to find differences. How can I install e.g. the RSEM package (http://toolshed.g2.bx.psu.edu/view/victor/rsem) on my local instance then? Is there a way to "pull" from the main tool shed so that I see the same data locally that's on the web? Thanks in advance, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics ☎ +44 1865 617481 ✉ benjamin.schuster-boeckler(a)ludwig.ox.ac.uk Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom

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Admin:Server:View data tables registry Internal Server Error
by Rodolfo Aramayo 16 Aug '13

16 Aug '13

Hi, On Galaxy d05bf67aefa6+ (stable) tip If I go to: Admin:Server:View data tables registry, I get: Internal Server Error with the following log: ##### URL: https://galaxy.tamu.edu/admin/view_tool_data_tables File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin.py', line 773 in view_tool_data_tables return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 957 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 969 in fill_template_mako return template.render( **data ) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/galaxy/galaxy-dist/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 '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/admin/view_data_tables_registry.mako.py', line 59 in render_body sorted_data_table_elem_names = sorted( trans.app.tool_data_tables.data_table_elem_names ) AttributeError: 'ToolDataTableManager' object has no attribute 'data_table_elem_names' ##### Similarly, If I go to: Reset metadata for tool shed repositories and click on the: Select/unselect all repositories Nothing happens, nothing is either selected or unselected Any Help/Ideas will be appreciated Thanks --R

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Multiple output files do not appear in history
by Christoph Malisi 15 Aug '13

15 Aug '13

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_… 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() ############################ ########################### <tool name="MultiOutTest" id="multiouttest"> <description>Multiple Outputs test</description> <command interpreter="python"> multiout.py -i $how_many $output1 $output1.id $__new_file_path__ </command> <inputs> <param name="how_many" type="integer" value="2" label="How many output files?"/> </inputs> <outputs> <data name="output1" format="txt"/> </outputs> <help> This is some help text. </help> </tool> #################################

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Job listing exception
by Kyle Ellrott 15 Aug '13

15 Aug '13

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 - <type 'exceptions.UnicodeDecodeError'>: '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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Display data in browser
by Gromobir 15 Aug '13

15 Aug '13

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

2 1

Searching on Tool Shed gives multiple revisions
by Peter Cock 15 Aug '13

15 Aug '13

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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Test Tool Shed down?
by Lionel Guy 15 Aug '13

15 Aug '13

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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galaxy-dev August 2013