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

Galaxy Data Sources and Dataset Collections
by Aaron Petkau 13 Nov '14

13 Nov '14

Hello, I've been spending a bit of time looking over Data Sources <https://wiki.galaxyproject.org/Admin/Internals/DataSources> for Galaxy. I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Galaxy, along with some user credentials. In this sense it would be similar to the GenomeSpace <https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999ed…> importer tool. However, instead of just exporting a set of files to a user's history, I'd like to be able to also automatically group these files into a dataset collection. I would also like to be able to link to these files instead of creating copies (which I think I can only do through a Data Library am I correct?). Ideally, I'd like to be able to use this tool as the first step in a workflow, which would allow me to import and structure the data needed for the rest of the workflow. Does anyone have any experience writing a similar tool? Is this possible in the current Galaxy version? Thanks, Aaron

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toolsheds down
by Evan Bollig PhD 12 Nov '14

12 Nov '14

Main and Test toolsheds are not resolving properly tonight... {u'status': u'error', u'error': u'Error attempting to retrieve installation information from tool shed http://testtoolshed.g2.bx.psu.edu for revision 7511823bdea1 of repository bedtools owned by iuc: <urlopen error [Errno -3] Temporary failure in name resolution>'} Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Repeats shown upside down on galaxy-central
by Peter Cock 12 Nov '14

12 Nov '14

Hi all, I'm running galaxy-central as my development server, and noticed what to me is a regression with repeat parameters, e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/… Read group: [+ insert read group] * 1: Read Group * 2: Read Group which on clicking becomes: Read group: [+ insert read group] * 2: Read Group * 1: Read Group This to me is upside down, the current behaviour on galaxy-dist is more natural (and also pluralises the group heading): Read Groups * Read Group 1 [Add new Read Group] which on clicking becomes: Read Groups * Read Group 1 * Read Group 2 [Add new Read Group] Is this a deliberate change? If so, why? Peter

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customize the Upload File tool form (version 1.1.4)
by Christophe Antoniewski 12 Nov '14

12 Nov '14

Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the "This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password)." I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine <http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-e…> 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniewski(a)upmc.fr http://drosophile.org

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large drill down selection UI component?
by Andrew Warren 12 Nov '14

12 Nov '14

Hi all, I was wondering if there were any existing implementations of, or any plans for, a drill down selection component that supports thousands of items? For example a taxonomy based drill down. Thanks, Andrew

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Tool shed environment dependency - HOW TO do this?
by Lukasse, Pieter 12 Nov '14

12 Nov '14

Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the "setup_r_environment" trick. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor package....the question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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rename output dataset in workflow - input dataset variable
by Jan Hapala 12 Nov '14

12 Nov '14

Hello, I want to rename ouput datasets in a workflow in such a way that the name contains the name of the input dataset. I could not find instructions in the manual (and this info is missing in the Workflow editor - would be really helpful there!). I tried #{input}, e.g. "stats on: #{input}" (with no quotes), but I keep getting just "stats on:" The variable is empty. When I use ${input}, I get a variable field in the workflow form (I do not want this). My G. instance: Galaxy changeset: d1e1beeb532239250396dd8fbdc0156508c6744e <https://bitbucket.org/galaxy/galaxy-central/commits/d1e1beeb532239250396dd8…> Can anyone help me, please? Jan

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picard and package_picard_1_56_0
by Evan Bollig PhD 11 Nov '14

11 Nov '14

Devteam: On 10/23 an update was posted to package_picard_1_56_0 that breaks tool Picard. Since 10/23, picard depends on package_picard_1_56_0, which in turn depends on picard 1.122.0, but that dependency makes absolutely no sense. Now when I run PairedReadMateFixer I get: #################### ## exit code=1; stdout= Error: Unable to access jarfile /FixMateInformation.jar #################### which appears to be caused by bad paths I don't understand toolshed logic for revisions: when I install tools with very specific revisions, the tool depends on very specific revisions of other tools. However, when I install a tool that depends on a package_*, the package has revision information, but it is ignored in favor of installing the LATEST revision of the package. If someone posts a buggy revision of a package_* to the toolshed, there is no way to avoid installing it until a fixed version is posted in its place. For example, when I run: python ./scripts/api/install_tool_shed_repositories.py --api XXXXXXXXXX --local http://127.0.0.1:8080 --url http://toolshed.g2.bx.psu.edu --name package_picard_1_56_0 --owner devteam --revision 61e41d21cb6f --tool-deps --repository-deps --panel-section-name "Other (Main Tool Shed)"' I expect package_picard_1_56_0:61e41d21cb6f to be installed, but instead I get package_picard_1_56_0:4a49481f29e7: ####### Response -------- /api/tool_shed_repositories/03501d7626bd192f name: package_picard_1_56_0 status: Installed tool_shed_status: {u'latest_installable_revision': u'True', u'revision_update': u'False', u'revision_upgrade': u'False', u'repository_deprecated': u'False'} deleted: False ctx_rev: 1 error_message: dist_to_shed: False tool_shed: toolshed.g2.bx.psu.edu installed_changeset_revision: 4a49481f29e7 uninstalled: False owner: devteam changeset_revision: 4a49481f29e7 id: 03501d7626bd192f includes_datatypes: False ####### Why ignore the package revisions? Btw, I did find an alternate (and working) package_picard_1_56_0 in the test toolshed, but why do I need to depend on the test toolshed for a production environment? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Galaxy Mailing Lists are moving
by Nate Coraor 11 Nov '14

11 Nov '14

Hello Galaxy Community, *Galaxy Mailing Lists are moving!* During the week of November 17-21, 2014, Galaxy mailing lists (including this one) will be migrated from lists.bx.psu.edu to lists.galaxyproject.org . This transition should be largely transparent to you, but there are a few things to be aware of: - List sender addresses and headers will change to reflect the updated domain: from bx.psu.edu to galaxyproject.org. Existing email filters you have set up may require adjustments. - Posts from lists.galaxyproject.org could be categorized as spam until you train your filtering method. - Mailing list archives and posting functionality will be briefly inaccessible during the migration. - The prior bx.psu.edu list posting email addresses will continue to accept email, which will be forwarded to the new list addresses. As always, you can manage your subscription for any Galaxy mailing list by following the link instructions at the bottom of this announcement. If you should notice any problems after the migration, please do not hesitate to let us know, via email to both "<list>-owner(a)lists.galaxyproject.org" (after the move) and to myself. Thanks, --nate, and the Galaxy Team

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Use of gzipped files in Galaxy Unit Tests
by Peter Cock 10 Nov '14

10 Nov '14

Hello all, Because Galaxy uses the upload tool internally for the inputs for function tests, it is possible to bundle gzipped versions of test inputs which saves space. For example, https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/… However, what I have just found is that this does not work for gzipped files as test outputs. Rather Galaxy seems to compare the (uncompressed) output from the tool to the expected output file as it is (i.e. still compressed). e.g. https://github.com/peterjc/pico_galaxy/commit/c8adfdf5d1f48c00ac72df967d2be… (I have only tested adding/removing the gzip compression on the output file locally) Is this deliberate? Peter P.S. I wanted point at the TravisCI output for that commit and its parent to show the output, - https://travis-ci.org/peterjc/pico_galaxy/builds/40203652 - https://travis-ci.org/peterjc/pico_galaxy/builds/40202182 However there appears to be an egg issue with the current galaxy-central branch: $ python scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File "scripts/fetch_eggs.py", line 46, in <module> c.resolve() # Only fetch eggs required by the config File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 192, in resolve if e.args[1].key != e.args[0].key: IndexError: tuple index out of range

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