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
Tools ( and tool related )
Modify tools contributed by Chungoo Park (firstname.lastname@example.org) 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.
- 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 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)
- 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.