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July 26, 2010 New Development News Brief

Here are the highlights of what you will get if you perform the following upgrade:

hg pull -u -r f94f1f2fa4be

Existing Feature Improvements

  • Modify tools contributed by Chungoo Park (cxp440@psu.edu) for Linear Discriminant Analysis.

  • Remove redundant 'Principal Component Analysis' tool.
  • Patch from Brad Chapman: Handle URLs for uploading in the case where Galaxy is served under a prefix and nginx is used to handle the uploads.
  • Updated indel analysis tools: fixed counting bugs in indel_analysis and improved help section; standardized CIGAR regex across tools; updated test files for several tools.
  • Reduce costly queries in the job runner, especially when tracking jobs in the database.
  • Fixes for generating viewports - these fixes eliminate some memory problems.
    • Add checks to get_estimated_display_viewport() methods for tabular data types to ensure datasets are valid before generating display links.
    • Now a maximum of 1MB is read from a line to determine the viewport; if a line greater than 10MB is encountered, then no viewport will be generated.
    • Additional fixes for certain cases when viewport was not determined properly for for WIG tracks and GFF.

PBS Cluster Support

  • Upgrade pbs_python to 4.1.0 and use PBS exit_status (if keep_completed is set) so we can detect PBS failures. This is a reapplication of 3786:48432330228e, which was backed out in a subsequent revision due to crashes experienced in pbs_python 2.9.8.


  • Remove mousewheel zoom (since scrolling window is more important), fix overview drag bug.
  • First selenium test for trackster.

Galaxy Sample Tracking

  • UI improvements - removed borders from the request page and added +/- icons for expand/collapse.

Galaxy Reports

  • Enhancements to the Job Information page
    • Add job.stdout to Job Info page in reports webapp ( patch from Assaf Gordon ), and change the previously displayed job.update_time to now be "Time To Finish", which is the total execution time of the job displayed in hh:mm:ss.
    • Patch to from Assaf Gordon to include job runner and job runner id on the job info page of the reports.

New Tools

  • New tool to 'Generate A Matrix for using PC and LDA'.

New Genome Indexes

  • Rhesus macaque (rheMac2)
  • Rattus rattus (rn4)
  • Sus scrofa (Sscrofa9.2/susScr2, Sscrofa9.58)

Bug Fixes

  • Fix bug so that fasta identifier produced by 'extract genomic dna' tool for GFF files is consistent with GFF coordinates.
  • Fix bug so that users not logged in can view accessible/published visualizations.