June 2015 - galaxy-dev - lists.galaxyproject.org

keep job output and scripts on failed tests
by Ryan G 15 Jun '15

15 Jun '15

I'd like to recommend a change. If jobs fail to run during functional tests, I'd like to keep the failed job files around to be examined. I added the following to do so: +++ scripts/functional_tests.py @@ -372,6 +372,7 @@ def main(): user_library_import_dir=user_library_import_dir, master_api_key=master_api_key, use_tasked_jobs=True, + cleanup_job='onsuccess' ) if install_database_connection is not None: kwargs[ 'install_database_connection' ] = install_database_connection

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Announcement: Disabling Tool Shed Testing Display
by John Chilton 14 Jun '15

14 Jun '15

Tool Developers, Last week I mentioned this in another thread - but I just wanted to re-iterate this in its own message in order to ensure more people see it. The Galaxy team will be regretfully disabling the display of tool test message on the main tool shed with next release - since they have been broken more often than not over the last year. We will hopefully be replacing it with an easier to reproduce locally, more robust solution by the end of year. Check out the details in the following message: https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-June/022204.html This will be a configurable option with the defaults such that local tool sheds should be unaffected. Thanks for Martin for working the implementation of this @ https://github.com/galaxyproject/galaxy/pull/337. -John

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docker-galaxy-stable tools fail
by Evan Bollig PhD 13 Jun '15

13 Jun '15

Not sure why, but these tools fail to install inside the docker-galaxy-stable Dockerfile build: indel_realigner unified_genotyper variant_select package_bedtools_2_19 bedtools I'm getting errors like these when executing "RUN install-repository": ############ [....] Galaxy is running. Processing: --url https://toolshed.g2.bx.psu.edu/ --name variant_filtration --revision da6e2503c62d --owner devteam HTTP Error 500: Internal Server Error {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0} 2015/06/13 03:56:34 The command [/bin/sh -c install-repository "--url https://toolshed.g2.bx.psu.edu/ --name variant_filtration --revision da6e2503c62d --owner devteam"] returned a non-zero code: 1 ############ Any thoughts? Cheers, -E -- Evan F. Bollig, PhD Scientific Computing Consultant, Application Developer | Research and User Services (RUS) Supercomputing Institute for Advanced Computational Research | msi.umn.edu University of Minnesota | umn.edu boll0107(a)umn.edu | 612-624-1447 | Walter Lib Rm 556

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Galaxy admin access
by Davenport, Aneisha 12 Jun '15

12 Jun '15

Hi, I work at the It service desk at the GRU Health and Science campus Ed Commons GB building and I have a customer trying to get admin access for the local installation of galaxy. We tried to follow the online instructions "In order to control your new Galaxy through the UI (installing tools, managing users, creating groups etc.) you have to become an administrator. First register as a new user and then give the user admin privileges like this: You add the Galaxy login ( email ) to the Galaxy configuration file (config/galaxy.ini). If the file does not exist you can copy it from the provided sample (config/galaxy.ini.sample). Note that you have to restart Galaxy after modifying the configuration for changes to take effect. # this should be a comma-separated list of valid Galaxy users admin_users = user1@example.com,user2@example.com" but we cannot alter the config/galaxy.ini file. Can you please give us assistance? Do you run in console or Terminal (this is a Macbook Air Laptop)? Aneisha Davenport

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picard_MarkDuplicatesWithMateCigar functional test failure
by Ryan G 12 Jun '15

12 Jun '15

The functional test for this tool fails. Looking at the XML wrapper, it looks like $comments is invalid....it doesn't exist anywhere else in the xml file. I know that comments can be specified multiple times however there is no way to get the comments fields to appear multiple times in the UI as far as I can tell. So, I changed it from #for $element in $comments: COMMENT="${element.comment}" #end for to COMMENT="${comment}" and the functional test passes.

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Functional test for BAM output
by Marius van den Beek 12 Jun '15

12 Jun '15

Hi list, I’ve been trying to write functional tests for a tool that produces BAM files as output. The tests run fine when using planemo locally, but not on the testtoolshed or on machines that do not have samtools installed. Apparently galaxy automatically tries to convert BAM to SAM to compare the output line by line, and so this fails. Surprisingly this is also true when comparing by size. This is the error: Tool id: bowtieForSmallRNA Tool version: bowtieForSmallRNA Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/drosof…) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 270, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in do_it raise e JobOutputsError: History item different than expected, difference (using diff): ( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/tmpQMbAfNoutput.bam ) Converting local (test-data) bam to sam failed: (cmd=[samtools view -h -o "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/local_bam_converted_to_sam_8Ym0af.sam" "/tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam"], stdout=[], stderr=[/bin/sh: 1: samtools: not found ]) Should samtools perhaps be added to the list of tools required for running galaxy? Best, Marius

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BioBlend Dependency Issues
by Medini Annavajhala 12 Jun '15

12 Jun '15

Hi All, Trying to install Galaxy via instructions online and having issues with fetching the eggs. Very similar issue to this thread: http://dev.list.galaxyproject.org/Bioblend-dependency-error-tt4664688.html#… , except that the dependency issue was "poster" instead of "mock". I tried the fixes in that thread (even trying to do run.sh in a clean virtual environment) but nothing worked. Any other ideas? Attached is the logfile showing the error messages. Thanks, -- Medini Annavajhala M.S./Ph.D. Candidate Dept. of Earth & Environmental Engineering Columbia University 500 W 120th St | MUDD 1045 NY, NY 10027

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delete many galaxy tools
by Alexander Vowinkel 12 Jun '15

12 Jun '15

Hi list, How can I delete multiple tools from my galaxy installation? So far I just know how to uninstall single ones through "Manage installed tool shed repositories" - But this is quite nasty if I want to uninstall many of them. Thanks, Alexander PS: I also posted this there: https://biostar.usegalaxy.org/p/12657/ what is the better place? Here or at the forum?

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Feature Request: Ability to specify a directory to read xml files for tool configuration
by Ryan G 11 Jun '15

11 Jun '15

Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of: <section id="myTools" name="Custom Tools"> <tool file="mytools/tool1.xml" /> <tool file="mytools/tool2.xml" /> .... </section> I can do: <section id="myTools" name="Custom Tools"> <tool file="mytools/*.xml" /> </section> I'd add this to Trello but unfortunately my company blocks the site.

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Couldn't download file
by Jingchao Zhang 11 Jun '15

11 Jun '15

Hi All, We have our Galaxy instance installed on local HPC with MySQL database. A user reported a issue with the tool "Merge BAM Files". The tool generated two files: .bam and .bai. The bam file can be downloaded with no problem. But when she was trying to download the index file (.bai) that should be associated with the generated .bam file, she got the following error: URL: https://hcc-galaxy.unl.edu/dataset/get_metadata_file?hda_id=284e19efbd6b170… File '/lustre/work/galaxy/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/lustre/work/galaxy/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/lustre/work/galaxy/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/lustre/work/galaxy/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/lustre/work/galaxy/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 276 in get_metadata_file return open(data.metadata.get(metadata_name).file_name) AttributeError: 'NoneType' object has no attribute 'file_name' I wonder if it's the file not being generated correctly or somehow MySQL lost track of it. Any help is appreciated. Regards, Jingchao

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