- galaxy-dev - lists.galaxyproject.org

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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Data Manager - BWA-MEM index
by Alexander Vowinkel 11 Jun '15

11 Jun '15

Hi, I'm trying to index some fasta files. They are uploaded in data library and I also loaded them into Data Manager history and my local history. But when I open the Data Manager, I can't choose my file. It says in "Source FASTA Sequence" only "No options available". Can somebody help? Best, Alexander

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job queue problem with cloud man
by Alexander Vowinkel 11 Jun '15

11 Jun '15

Hi list-members, I have a Cloud Man instance on amazon. I did minimal adaption (installing some tools, adding an index) I'm currently running only a master, which is allowed to run jobs. I have now 3 jobs saying: "This job is waiting to run" But in the CloudMan console it says: "Worker status: Idle: 0 Available: 0 Requested: 0" Also condor_q gives 0 jobs. Where is the problem? I already restarted the galaxy service via the admin console... Can someone help me to find whats going wrong? Thanks! Alexander PS: I'm running different job types (one is just "Add column") PPS: "Upload File" jobs are working

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Bismark doesn't end and blocks the server
by C. Ch. 10 Jun '15

10 Jun '15

Hi all, I have a clean local install of galaxy from git (commit: 40b69cb948eed2cece82a32dfc5c6116414ab97c).I've installed bismark and I get an error message (see below) if I do not choose the 'sort' option.I have the impression that this might be related more to galaxy than to bismark itself. The result is that the server gets blocked and the only solution is to restart galaxy. Any help is appreciated!Cristian The error message:galaxy.datatypes.metadata DEBUG 2015-06-05 11:14:12,514 setting metadata externally failed for HistoryDatasetAssociation 1305: External set_meta() not called[bam_index_core] the alignment is not sorted (HWI-ST278R:398:C1WUTACXX:3:1101:9378:2574): 2-th chr > 1-th chr[bam_index_build2] fail to index the BAM file.

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