Commits

Author Commit Message Labels Comments Date
Nate Coraor
Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.
Kanwei Li
Grouping tool: use system numpy if provided, otherwise use bundled numpy egg
Kanwei Li
Fix sam2interval.py bug due to tab spacing
jeremy goecks
Trackster: route track drawing through requestAnimationFrame framework.
Kanwei Li
Simplified Custom Builds page... show less by default
Kanwei Li
Tool versioning: now store version information in hda/ldda tables. Information is kept when copied between hda/ldda, and now displayed in the "Show Info" pages for hdas and lddas.
jeremy goecks
Trackster: remove throttling during dynamic filtering because it's not needed with requestAnimationFrame.
jeremy goecks
Trackster: make it possible to set features' transparency based on attribute values.
Greg Von Kuster
Add the ability to switch between tool shed repository revsions when viewing tool metadata.
Nate Coraor
Decrease user disk usage when files are removed from disk by the cleanup_datasets.py.
Daniel Blankenberg
Allow FASTQ Groomer tool to work on Color Space files that contain a fake/dummy quality score for the adapter base (e.g. files obtained from the SRA). The Groomer will remove the dummy/fake quality score from the read.
Daniel Blankenberg
Add FIMO to tool_conf.xml.sample.
Daniel Blankenberg
Add FIMO tool from MEME suite.
Nate Coraor
Fix FTP upload when uploading only a single file and its name contains a comma. util.listify assumes that a string with commas should be split into a list, so don't use listify for this value. Thanks Ilya Chorny.
Daniel Blankenberg
pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.
Nate Coraor
Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs.
Kanwei Li
Spacing fix
Ross Lazarus
WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...
Greg Von Kuster
Add the ability for authenticated tool shed users to contact the owner of a repository via email.
Nate Coraor
merge
Nate Coraor
Closed branch job_scripts
Branches
job_scripts
peterjc
Catch problems creating job script
Branches
job_scripts
jeremy goecks
Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/).
Nate Coraor
Quota display nice_size bugfixes.
Greg Von Kuster
Enhancements and fixes for working with versions of repository tools in the tool shed.
Nate Coraor
Don't count library datasets against the creating user upon dataset creation.
Nate Coraor
Decrease disk usage and actually remove datasets (if applicable) when purging a history.
Nate Coraor
Monkeypatch BigInt(eger) into SQLAlchemy 0.5 and make the bytes column in the quota table a bigint.
Nate Coraor
Backed out changeset 6ca0a743296b, Alchemy 0.5 has no BigInteger...
Nate Coraor
Make the bytes column in the quota table a bigint
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