September 2014 - galaxy-dev - lists.galaxyproject.org

IE 11 issues
by Sajdak, Doris 25 Sep '14

25 Sep '14

We are having issues with using Galaxy in Internet Explorer 11 (these work fine in Chrome & Firefox). 1. The jobs queued and history doesn't display unless you refresh the browser window. Clicking the history reload icon doesn't work. 2. If I click to edit something in the history, the tabs aren't clickable. Attributes are displayed but I can't click on Convert Format, Datatype, or Permissions. Anyone else having this problem? I apologize if this information is documented somewhere but I was unable to find it. Thank you for your assistance, Dori ********************************** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu **********************************

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New post action with workflows : DeleteIntermediatesActionOutput
by julie dubois 24 Sep '14

24 Sep '14

Hi all, I'm not sure how do this post-action act . I've been make some test and it's very confused for me. First, can this post-action be used on output which are used on other steps of the workflow ? if yes, I suppose that galaxy wait for end of use of this output before deleting. Second, must I higlight the snowfalke of this output to permit its deletion or must I keep the snowflake in grey ? I post this question in galaxy-dev because I've added this post-action on several outputs in my workflow and it has had no effect on my outputs. And when I open the .ga file which describe my workflow, I've seen just one of this post-action in one output. Thanks. Julie

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Missing configuration and location files automatic creation
by Julien Seiler 22 Sep '14

22 Sep '14

Hi all, I have notice that the run.sh script is creating automatically all missing configuration and location files to make sure Galaxy can work properly at first launch. However, the script is not taking care of the actual settings of an existing universe_wsgi.ini file. As a result, if the universe_wsgi.ini file says that job_conf.xml is located at foo/bar location, the run.sh will create a job_conf.xml file at the root of the galaxy source code anyway. I'm thinking of improving the run.sh behavior to respect file path declared in an existing universe_wsgi.ini file in order not to create unused config or location files. I have currently started to implement this behavior in a small Python script (more handy than pure sh). What do you think about this concern ? Should I go for a pull request at any point ? Regards, -- Julien @julozi

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Workflow param error leads to template error
by Paul-Michael Agapow 19 Sep '14

19 Sep '14

Looking for pointers on what might be causing this problem: A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends: Module workflow_run_mako:232 in render_body >> for ic in oc.input_step.module.get_data_inputs(): AttributeError: 'WorkflowStep' object has no attribute 'module' After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render "run.mako" flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring? Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't) Hosting OS: CentOS 6 ------ Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency (UK) ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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find bam index files
by Ulf Schaefer 19 Sep '14

19 Sep '14

Dear all For each bam file in my history I can download the associated bai (bam index) file. I assume these files are stored somewhere under /mount/galaxy/database/files/_metadata_files. Correct? Is there an easy way to find the bam index file for a bam file, given only the internal file name of the bam (e.g. /mont/galaxy/database/files/089/dataset_89231.dat)? I am asking because I would like to use the files_to_ftp tool to automatically download bams together with their associated indices. Thanks Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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Question about uploading a large application to the tool-shed
by George Weingart 18 Sep '14

18 Sep '14

Hello, I have an application that is working perfectly in our local Galaxy (Not using tool-shed) I would like to upload it to the tool-shed (I have uploaded other applications to the tool-shed before) The size of the directory (//usr/local/galaxy-dist/tools/metaphlan2) is 2.1 GB and after I tar it it is 1.1 GB. The question: Is it too big to be uploaded to the tool-shed? Thanks! George Weingart

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Problem writing functional tool tests with 'repeat' & 'conditional' tags
by Peter Briggs 17 Sep '14

17 Sep '14

Hello all I'm experiencing problems with specifying some tests for a Galaxy tool I've written, which are related to setting the value of a 'conditional' parameter that is defined within a 'repeat' tag. The bones of the tool XML look like: ... <repeat name="operations" title="..." min="1"> <conditional name="operation"> <param name="name" type="select" label="..."> <option selected="true" value="SLIDINGWINDOW">Sliding window trimming...</option>  </param> <when value="SLIDINGWINDOW"> ... When I run the functional tests I get: base.twilltestcase: ERROR: In submit_form, continuing, but caught exception. Traceback (most recent call last): File "XXXXX/galaxy-dist/test/base/twilltestcase.py", line 1910, in submit_form for value in kwd[ control.name ]: KeyError: 'operations_0|operation|name' Is there a way to specify the the value in the tests? I've tried both <param name="operations_0.operation.name' value="..." /> and <param name="operations_0|operation|name' value="..." /> in my <test>s, but neither form seem to change the exception from the tests. Any suggestions are greatly appreciated! Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Problem with tool dependencies when running functional tool tests
by Peter Briggs 17 Sep '14

17 Sep '14

Hello again As an addendum to my previous message, I'm also having general problems running the functional tests for any tool, due to unresolved tool dependencies. For example if I clone and configure a fresh galaxy-dist instance and install the FastQC tool from the main toolshed, and then run e.g.: $ export GALAXY_TOOL_DEPENDENCY_DIR=/home/pjb/galaxies/kellerman/tool_dependencies ; sh run_functional_tests.sh -installed In the stdout I see output like: ... galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'FastQC' galaxy.tools.deps: WARNING: Failed to resolve dependency on 'FastQC', ignoring ... and in the run_functional_tests.html report I see: Traceback (most recent call last): File "/home/pjb/galaxies/kellerman/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/e28c965eeed4/fastqc/rgFastQC.py", line 204, in <module> assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /fastqc As far as I can make out I'm correctly following the instructions at https://wiki.galaxyproject.org/TestingInstalledTools so I'm wondering if anyone can point out what it is that I'm missing. No doubt it's blindingly obvious, but I just can't see it. Thanks again for any help Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Dependencies within dependencies
by Christophe Antoniewski 17 Sep '14

17 Sep '14

I am trying to move the package_r_3_0_3 repository owned by devteam from the main toolshed to our local toolshed. This does not work as some dependencies required for package_r_3_0_3 are not exported (export capsule) and not included in the archive. For instance, package_freetype_2_5_2 and package_libpng_1_6_7 are present in the capsule and thus moved to the local toolshed, but not package_readline_6_2, package_cairo_1_12_14 and package_pixman_0_32_4. Is it a bug (I would expect a sort of recursivity in the export process) or did I miss some logics behind this ? And do we have to manually export-import the missing dependencies to the local toolshed ? Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 christophe.antoniewski(a)upmc.fr http://bio-dev.snv.jussieu.fr/ Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org http://www.sciencesenmarche.org/

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Main tool shed installation issues
by Yves Gagnon 17 Sep '14

17 Sep '14

Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : Error Traceback: ⇝ URLError: <urlopen error [Errno -2] Name or service not known> Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?reposi… Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves

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