1. jianma
  2. Cistrome-Harvard-dev

Commits

Author Commit Message Date Builds
Tao Liu
Add Cistrome configuration of tools_conf.xml and universe_wsgi.ini.
Tao Liu
Add Cistrome tools.
Tao Liu
Add Cistrome tools: peakcalling, motif, liftover, expression, correlation and ceas.
Greg Von Kuster
When rendering the contents of a data library, make sure a LibraryDataset has an associated LibraryDatasetDatasetAssociation. There should always be an ldda, but some users running their own instances have reported that some of their LibraryDatasets are missing these associations.
Greg Von Kuster
Fix bug when rendering the contents of a data library - render the options for acting on multiple datasets if the library includes accessible datasets at any level in the hierarchy rather than if it only includes them in the root folder.
jeremy goecks
Trackster: fix max chrom length.
Kanwei Li
trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization.
Daniel Blankenberg
Add a Line/Word/Character count Text Manipulation tool.
Nate Coraor
lazy load jobs for job recovery and a bugfix for administrative job stops when tracking jobs in the database.
jeremy goecks
Trackster: remove bottom border from tiles to prevent poor spacing in summary tree view.
Nate Coraor
Bug fixes for missing scrollbars on OpenID pages.
Kanwei Li
Add len_file_path configurable to specify where chrom .len files are stored
rc
Bug fix: when no library is associated with the sample link to display datasets is disabled.
jeremy goecks
Trackster: better handling when data has a message -- (a) if there's data, show it; and (b) add border to all canvas elements so that they line up when messages are shown and error borders are drawn.
jeremy goecks
Fix attribute bug in cuffcompare wrapper.
jeremy goecks
Trackster: increase summary tree track height so that max label does not overlap data.
Greg Von Kuster
Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.
rc
Bug fix in find samples results page
jeremy goecks
Fix bug in extract_genomic_dna.py so that comment lines are correctly handled.
Nate Coraor
Fix for PBS job runner importing itself instead of pbs_python.
Nate Coraor
Fix infinite loop setting up locales.
Kanwei Li
trackster: - Fix bug where tiles were not aligning correctly because of inconsistent w_scale - Fix tracks with errors or no data not having right background - Refactoring
Nate Coraor
Instead of raising in exception, default to english if a locale is set by the client but not installed on the server.
Nate Coraor
The Galaxy-side job runner for execution via LWR, a light weight cluster setup written by John Chilton. For more information on implementing the cluster, see: https://bitbucket.org/jmchilton/lwr/
Nate Coraor
Handle bugs encountered when fetching an egg during a version conflict and a sys.path item has been removed.
Nate Coraor
Fix a minor bug which mad it completely impossible to run a job.
Nate Coraor
Make loading of job runners dynamic. Changes to lib/galaxy/config.py and lib/galaxy/jobs/__init__.py are no longer required. Existing runners which are not part of the Galaxy source will need to define the class name to instantiate in the __all__ list in the runner. See the included runners for an example.
guru
Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool
jeremy goecks
Fix searching functionality and labels in published item grids.
Kanwei Li
trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available
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