Development News Brief

January 27, 2012

Get Galaxy

getgalaxy

getgalaxy.org

  • new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
  • upgrade: % hg pull -u -r 26920e20157f

Run Cluster Jobs as the Real User

  • On systems where Galaxy users are guaranteed to match users on the system, it may be preferable to run jobs on the cluster as the system user matching the Galaxy user, rather than the system user under which Galaxy started.
  • This method of job ownership is now possible. To learn how to set it up and use it, please see the documentation at: Admin/Config/Performance/Cluster
  • Thank-you Ilya Chorny for contributing the code for this very popular enhancement request!

New "Create Schema" Function

  • The Galaxy database schema can now be created without starting the Galaxy server.
  • To do so, simply execute create_db.sh in the top-level galaxy-dist/ directory.
  • Thank-you John Duddy for contributing the code for this feature that helps makes Galaxy customization even easier!

Job Management

  • DRMAA runner: DrmCommunicationException will no longer cause a job to fail. Instead, the job will return to the monitored job queue and be checked again.
  • Use temporary files instead of pipes for local job execution - prevents tools from hanging when they write large amounts of data to STDOUT/STDERR.

Tools

Many tools have been recently upgraded. Please review Admin/Config/Tool Dependencies and Admin/Config/Tool Dependencies for these and other recently updated Tool Dependencies.

  • SAMtools:

    • All wrappers in group accept versions 0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred.

    • Exceptions:

      • flagstat (existing) requires versions 0.1.16-0.1.18.
      • Mpileup (new) requires versions 0.1.16-0.1.18.
      • Pileup (existing) requires versions 0.1.12-0.1.16, with 0.1.16 strongly preferred and tool dependency directory configuration (if upgrading other SAMtools to 0.1.18).
    • Galaxy Main is running SAMtools version 0.1.18 for all with the exception of Pileup version 0.1.16.
  • Updated TopHat tests for version 1.4.0.
  • Updated Cufflinks, CuffCompare, CuffDiff tests for version 1.3.0.
  • Better error reporting in Cufflinks.
  • Enhance Picard SamToFastq to allow read group aware processing.
  • Properly set the temporary directory when using the SAM merge tool. Thank you Lance Parsons!
  • Properly set the temporary directory when using the Picard tools. Thank you John Chilton!

Galaxy Track Browser (GTB)

  • Trackster Bug fixes: filter drawing bug, summary tree display, embedded visualizations.
  • Do not find valid chroms because this is computationally expensive and not currently used.
  • Provide icon to randomly set color in drawable configuration.

  • Multi-track dynamic filtering.

Workflows

  • Improve language in 'Import workflow' dialog.
  • Input Dataset steps will now again properly filter appropriate input datasets based on subsequent tool input types. This fixes the regression introduced in 6329:ab90893a7cf5.

Data and Libraries

  • When uploading compressed files to a data library, remove the compressed file extension only if copying files into Galaxy's file store.
  • Add Eland datatype support and generic XML datatype to the sample configuration file. Another thank-you to John Duddy!

Tool Shed

  • Tool Shed fixes:

    • Fix for handling a tool data table entry when uploading to a tool shed repository.
    • Reset all metadata on all changeset revisions of a tool shed repsoitory whenever a new change set is introduced. This will result in a more standardized set of valid changeset revisions that can be installed.
    • Fix for generating workflow metadata and viewing workflows in tool shed repositories.
    • Fix for searching for workflows in the tool shed.
  • Deactivating and uninstalling tool shed repositories installed into a local Galaxy instance

Bug Fixes

bugs
* Python 2.5 support was broken in the last stable release, this has been fixed * A broken unit test under 2.5 will not be fixed until the next release, however - this can safely be ignored. * A fix to not use math.isnan because it is not compatible with python 2.5 has been made. * Fix for setting up column assignments for dynamic options with respect to tool data tables when the index file is missing causing tools to fail to load. * Have **[GOPs Concatenate](/learn/interval-operations/)** tool always respect the provided strand column. Fixes issue seen when providing intervals with a chrom/start/stop in column 5 and strand was not set. * On edit attributes page, make the info field a text area. Fixes lost new line characters in field when changing name. * The Object Store unit test that was failing in the last stable release has been fixed.

About Galaxy

GalaxyProject.org

The GalaxyTeam is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.

Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State, and Emory University.

Join us at Twitter @galaxyproject

Jennifer Jackson, Galaxy Team. Posted to DevNewsBriefs on 2012-01-27