August 2013 - galaxy-dev - lists.galaxyproject.org

Editing workflow - automatic update changes not saved?
by Peter Cock 21 Aug '13

21 Aug '13

Hi all, I'm trying to update one of my saved workflows which was created using an old version of the filter tool BEFORE this tool had the option "Number of header lines to skip". In order to get rid of the nag message on using the tool, I want to re-save the workflow using the default 0 for this. This missing parameter was also causing problems trying to import the *.ga file for this old workflow, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016223.html The (now out of date) copy of the Workflow is on the Tool Shed, but to update it I am working on the same Galaxy instance used to create it (where TMHMM and SignalP were manually installed and have been updated since): http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow 1. Log into Galaxy 2. Click on workflows (top menu) 3. Find my workflow, select "Edit" from the dropdown menu 4. Observe warning: Workflow loaded with changes Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. Step 3: Filter No value found for 'Number of header lines to skip', used default Step 6: Filter No value found for 'Number of header lines to skip', used default 5. Click on these workflow steps, verify this new parameter is set to zero. 6. Save the workflow, observe blue progress bar pops up. 7. Close the workflow 9. Save the workflow to disk as a *.ga file 8. Open the workflow again for editing Expected result: New parameter recorded, and tool versions updated. Actual result: No change, same warning appears. No sign of the new setting in the freshly save *.ga file. Tool versions not changed. Workaround: Change the default values to one ("1"), save, close, reopen, no warning, change values back to zero ("0"), save, close, reopen, Happy. Is this simply a bug where the workflow editor wrongly assumes no changes have been made (despite there being two major types of change - the new header_lines parameter, and the versions of the tools)? Peter

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Error granting permissions on new Tool Shed repository
by Peter Cock 21 Aug '13

21 Aug '13

Hi Greg, Dave, While logged into the Test Tool Shed as 'iuc', I just created a new (empty) repository: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 See background discussion on this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html As 'iuc', I then tried to grant write access to myself ('peterjc') and Bjoern ('bgruening') as we are both IUC members and working on the Galaxy BLAST+ project: https://github.com/peterjc/galaxy_blast The default dummy entry "Select One" entry was still being displayed. I clicked 'Grant Access' and got this error: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc57… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2072 in manage_repository >> user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) Module galaxy.web.security:60 in decode_id >> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) Module encodings.hex_codec:42 in hex_decode >> output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found extra data full traceback text version This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. -- I tried again but explicitly removed the dummy entry "Select One" and it seemed to have worked. I am running Firefox v22.0 on Mac OS X. Regards, Peter

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Workflow action summary confusing, repeats "Hide this dataset"
by Peter Cock 21 Aug '13

21 Aug '13

Hi all, I have found two potential bugs with how workflow actions are described to the user when running a workflow. I am looking over the "run workflow" dialogue for this workflow, (I currently get a warning due to the filter tool having a new "Number of header lines to skip" option) http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow I manually imported the *.ga file due to issues with the Tool Shed workflow import, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016209.html I am running the latest galaxy-dist, $ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user: greg date: Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user: Dave Bouvier <dave(a)bx.psu.edu> date: Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files. -------------------------------------------------------------------------- For step 2, the details view says: Actions: Hide this dataset. Hide this dataset. I find that confusing, and initially thought there might be a bug or duplicated action. Actually it is just a misleading summary as this tool can produce TWO outputs: "post_job_actions": { "HideDatasetActionoutput_neg": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_neg" }, "HideDatasetActionoutput_pos": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_pos" } }, Perhaps the "Hide this dataset" message could be less ambiguous by using the output variable names (as in some of the other action descriptions)? There are similar problems with the next steps too. -------------------------------------------------------------------------- Steps 6 and 7 are also odd. For step 6 the details view says: Actions: Hide this dataset. Rename output 'out_file1' to 'Filtered SignalP results'. Hide this dataset. Rename output 'out_file1' to 'Filtered SignalP results'. Likewise for step 7, Actions: Hide this dataset. Rename output 'output_pos' to 'Secreted proteins'. Hide this dataset. Rename output 'output_pos' to 'Secreted proteins'. Again, there seems to be a duplication of the messages. It should be hiding one output, and renaming the other, e.g. "post_job_actions": { "HideDatasetActionoutput_neg": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_neg" }, "RenameDatasetActionoutput_pos": { "action_arguments": { "newname": "Secreted proteins" }, "action_type": "RenameDatasetAction", "output_name": "output_pos" } }, -------------------------------------------------------------------------- In some ways this is just a harmless cosmetic issue, but it does seem confusing to me. Thanks, Peter

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Troubleshooting file uploads (to Data Library)
by Clare Sloggett 21 Aug '13

21 Aug '13

Hi, I am having trouble uploading files to a Data Library, and I'm not sure where to begin troubleshooting. I'm uploading from a URL (but I had a similar issue from the desktop). The symptom is that the datasets in the library have the message "This job is queued" and never seem to progress. I am one of very few users of this instance (quite likely the only user right this moment). I don't think the server is busy, so I'm not sure why the files uploads don't seem to be proceeding. How can I investigate further? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

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DESeq for Galaxy
by Sridhar Srinivasan 21 Aug '13

21 Aug '13

Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar

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Tool Shed upload/migration revision checking bug?
by Peter Cock 21 Aug '13

21 Aug '13

Hi Bjoern & Greg, The Biopython package looks OK on the test tool shed, http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 This includes the lines: <package name="numpy" version="1.7.1"> <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="matplotlib" version="1.2.1"> <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> Note that we plan to update those dependencies to point at the IUC account, not Bjoern's personal account. However, on the main Tool Shed something is broken with the dependencies lacking relevant revisions: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 <package name="numpy" version="1.7.1"> <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="matplotlib" version="1.2.1"> <repository name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> My guess is the revisions failed because there is no such repository on the main Tool Shed (they do exist under the new IUC user through, while on the Test Tool Shed they exist under both usernames for now). Bjoern, do you remember if this was a manual upload to the Main Tool Shed, or done via the migration script? Greg, if this was uploaded manually, the reference to non-existent repositories should have shown up as an error. If this was migrated, was there no error message? Bjoern, are you happy to update both the test & main repositories to point at the IUC packages now? Or should I do that myself? Thanks, Peter

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Biopython dependency on matplotlib
by Peter Cock 21 Aug '13

21 Aug '13

Hi Bjoern (& Greg), RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 I'm wondering why in the Biopython package dependencies matplotlib is currently marked as prior installation required? i.e. <package name="numpy" version="1.7.1"> <repository changeset_revision="c75482be1d3a" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="matplotlib" version="1.2.1"> <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> Biopython needs NumPy pre-installed because Biopython has some C code which must be compiled against the NumPy headers. However, all the other Biopython Python dependencies are soft in the sense that the 3rd Python libraries just need to be available at run time (e.g. via $PYTHONPATH). Have I misunderstood the function of the Galaxy Tool Shed term prior_installation_required, or can we omit this and have it default to prior_installation_required="False" for matplotlib (and other similar cases)? ------------------------------------------------------------------ More generally, if that is the case, I would probably opt to make the Biopython package only depend on numpy, and leave declaring soft dependencies (or recommended packages in the terminology of some Linux distributions) down to the package/tool calling Biopython. For instance, my sequence manipulation tools which use just core Biopython can depend on just the main Biopython package. Another tool which uses Biopython and matplotlib to produce a graph would depend on both Biopython and the matplotlib packages. Another tool which uses Biopython's GenomeDiagram to produce a figure would depend on both Biopython and the (not yet written) ReportLab packages. etc. Peter

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Implementing blend4j
by Eric Kuyt 20 Aug '13

20 Aug '13

Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

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Re: [galaxy-dev] Apache authentication UCSC error
by Shane Sturrock 20 Aug '13

20 Aug '13

OK, I've solved it. The issue with display_as location remains and I still have to put the Allow from directives in the / location but I have been able to get UCSC working again and I'm completely to blame so maybe I should keep quiet but no, in the spirit of sharing one's idiocy here it is folks. I was looking at user account admin a few weeks back and noticed some old users before I switched to the AD authentication so I thought it would be a good idea to clean them out. Turns out there is an account called remote_display_server which I had deleted and that was the key because removing that triggered the user_disabled message that UCSC was seeing (duh!) so re-enabling that fixed the issue (double duh!) I will now sit in the corner with a dunce cap on for the rest of the day..... Shane -- For urgent cases, contact support(a)biomatters.com Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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Name of downloaded file
by Alexandre Defelicibus 20 Aug '13

20 Aug '13

Hi everyone, Is there a way to set the name of the file which is downloaded by the user? The output name is, for example, Results.zip, but when I download the file, the name cames as Galaxy-100[Results.zip].data. I would like to receive the file with the name Results.zip. Is it possible? Best regards, -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP

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