- galaxy-dev - lists.galaxyproject.org

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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Integration with remote SAAS
by Joe Stubbs 20 Aug '13

20 Aug '13

Hello, I'm working on a project to integrate a Galaxy instance with a remote software execution service. The service maintains a catalogue of applications, storage and execution hosts, files (input and output) and jobs (submitted, executing, finished, etc) all manageable through REST endpoints. For the integration, I'd like apps, datasets and jobs in the service to be available through Galaxy. RIght now, I'm querying the service to retrieve the catalogue of apps available to a user and, after some conversion, inserting them into the Galaxy toolbox. For these apps, jobs are submitted via the REST API and executed on the execution host registered in the service. I'm currently polling a status endpoint in the service to keep Galaxy updated with the job's status. I'd like the I/O to be seamless for the users, so that datasets generated from "native" Galaxy tools/jobs can be used as inputs for service apps and vice versa. Similarly, I would like to take advantage of Galaxy's data viewer for datasets generated by remote jobs. Since the service can handle files published to URLs, I was looking into that approach. It looks like Galaxy has some support for this -- perhaps using redirect params? Is that right, and if so, is there documentation on what is currently supported in Galaxy? Does this seem like the best approach? Among other wish list items, it would be nice if the toolbox (or at least the catalogue of apps in the service) could be refreshed real-time. Right now they are only being added at server start up. Quite generally, I would welcome any comments or suggestions on the overall integration approach as I am fairly new to Galaxy. Thanks in advance, Joe -- Joe Stubbs Research Engineering Scientist Associate Texas Advanced Computing Center University of Texas, Austin

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Bullet points not showing in README.rst on Tool Shed
by Peter Cock 20 Aug '13

20 Aug '13

Hi all, I'm having a problem with bullet point lists in my README.rst file not rendering nicely on the (main and Test) Tool Shed. This example of mine shows the bullet points fine on GitHub's rendering (two bullet lists examples): https://github.com/peterjc/picobio/blob/424747ecccf5cce6ce327754e6f8e57a594… However, on the Tool Shed the bullet points are missing: http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow/de29af5da… Here is the relevant reStructuredText documentation: http://docutils.sourceforge.net/docs/user/rst/quickref.html#bullet-lists As per the documentation, I have a blank line before and after the bullets, and I am using one other three valid bullet characters ("*", rather than "-" or "+"), e.g. * 89 RXLRs using Whisson et al. (2007) * 124 RXLRs using Win et al. (2007) * 162 RXLRs using Bhattacharjee et al. (2006) In fact, looking at the HTML source on the Tool Shed it has correctly rendered as an unordered list: <ul class="simple"> <li>89 RXLRs using Whisson et al. (2007)</li> <li>124 RXLRs using Win et al. (2007)</li> <li>162 RXLRs using Bhattacharjee et al. (2006)</li> </ul> Is there a bug in the default Tool Shed CSS which is hiding the bullet points? Thanks. Peter

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Error when I will set "set at runtime" in a workflow
by Ramon Tiburski 20 Aug '13

20 Aug '13

I have a tool that uses two dates to fetch data in a database. I am using a parameter type called "datetime" in the field "type". It uses javascript and allows a date to be selected through a calendar. When I use it as a tool works perfectly, but when I try to use the workflow got an error. When I check the "Set at runtime" I got the following error: Server Error URL: http://localhost:8080/workflow/editor_form_post Module paste.exceptions.errormiddleware:144 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:185 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator >> return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:607 in editor_form_post >> 'tool_state': incoming.pop("tool_state") KeyError: 'tool_state' and I can not create the workflow. What can I do? Thank you

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Getting data from a database to create a dynamic combo box
by Ramon Tiburski 20 Aug '13

20 Aug '13

Hi, I need to create a combo box that will take data from a database dynamically. How could I do this? Thank you

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