 Kanwei Li
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1502eed32f
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sam2interval: Add read_name column
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2011-08-24 16:43:02 -04:00 |
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Nate Coraor
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eb036815cb
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Fix sending mail when the receipient is a list (as in sample tracking mail routines).
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2011-08-24 15:33:07 -04:00 |
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Jeremy Goecks
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e81c4ef6a8
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Pack scripts.
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2011-08-24 14:42:56 -04:00 |
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Nate Coraor
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3cbde2e760
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Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.
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2011-08-24 14:38:29 -04:00 |
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Kanwei Li
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068ef1df40
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Grouping tool: use system numpy if provided, otherwise use bundled numpy egg
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2011-08-24 13:58:48 -04:00 |
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Kanwei Li
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ad24f8c1dc
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Fix sam2interval.py bug due to tab spacing
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2011-08-24 13:14:49 -04:00 |
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Jeremy Goecks
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9985d54d98
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Trackster: route track drawing through requestAnimationFrame framework.
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2011-08-24 10:19:38 -04:00 |
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Kanwei Li
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4d01729416
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Simplified Custom Builds page... show less by default
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2011-08-24 01:11:54 -04:00 |
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Kanwei Li
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eb6bf73cab
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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.
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2011-08-24 00:45:31 -04:00 |
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Jeremy Goecks
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d073792e38
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Trackster: remove throttling during dynamic filtering because it's not needed with requestAnimationFrame.
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2011-08-23 17:27:58 -04:00 |
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Jeremy Goecks
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174e8d3c48
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Trackster: make it possible to set features' transparency based on attribute values.
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2011-08-23 17:21:37 -04:00 |
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Greg Von Kuster
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b04b96dc53
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Add the ability to switch between tool shed repository revsions when viewing tool metadata.
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2011-08-22 16:31:50 -04:00 |
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Nate Coraor
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3a1526ac8a
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Decrease user disk usage when files are removed from disk by the cleanup_datasets.py.
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2011-08-22 16:19:49 -04:00 |
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Daniel Blankenberg
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90e695c9aa
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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.
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2011-08-22 16:07:23 -04:00 |
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Daniel Blankenberg
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ed79503fe7
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Add FIMO to tool_conf.xml.sample.
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2011-08-22 14:58:51 -04:00 |
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Daniel Blankenberg
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8768351b99
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Add FIMO tool from MEME suite.
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2011-08-22 14:52:11 -04:00 |
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Nate Coraor
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cdd29d1781
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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.
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2011-08-22 14:47:10 -04:00 |
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Daniel Blankenberg
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aec47aa2a9
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pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.
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2011-08-22 14:03:57 -04:00 |
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Nate Coraor
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83163908e8
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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.
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2011-08-22 10:45:22 -04:00 |
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Kanwei Li
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a9370f1b72
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Spacing fix
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2011-08-20 02:56:33 -04:00 |
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Ross Lazarus
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d178424fc9
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WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...
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2011-08-20 14:27:30 +10:00 |
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Greg Von Kuster
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b58f2a36b4
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Add the ability for authenticated tool shed users to contact the owner of a repository via email.
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2011-08-19 14:37:51 -04:00 |
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Nate Coraor
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8f95c32de2
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merge
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2011-08-19 13:30:36 -04:00 |
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Nate Coraor
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e7bf8e613e
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Closed branch job_scripts
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2011-08-19 13:30:21 -04:00 |
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Jeremy Goecks
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781cef42bd
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Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/).
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2011-08-18 14:20:48 -04:00 |
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Nate Coraor
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388c1a02a4
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Quota display nice_size bugfixes.
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2011-08-18 14:01:28 -04:00 |
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Greg Von Kuster
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7114d7a575
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Enhancements and fixes for working with versions of repository tools in the tool shed.
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2011-08-18 13:51:02 -04:00 |
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Nate Coraor
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b2e7ec594b
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Don't count library datasets against the creating user upon dataset creation.
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2011-08-18 13:13:35 -04:00 |
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Nate Coraor
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6f9701bb41
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Decrease disk usage and actually remove datasets (if applicable) when purging a history.
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2011-08-18 13:08:39 -04:00 |
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Nate Coraor
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a32371d794
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Monkeypatch BigInt(eger) into SQLAlchemy 0.5 and make the bytes column in the quota table a bigint.
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2011-08-18 11:08:47 -04:00 |
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Nate Coraor
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fb6b91aaab
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Backed out changeset 6ca0a743296b, Alchemy 0.5 has no BigInteger...
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2011-08-17 16:32:09 -04:00 |
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Nate Coraor
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01e26cb092
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Make the bytes column in the quota table a bigint
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2011-08-17 16:25:34 -04:00 |
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Greg Von Kuster
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ab16573078
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Add the ability for tool shed users to select repository revisions whose tools can all be successfully loaded into a Galaxy instance in order to view / preview / download various tool versions from a specified repository.
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2011-08-17 11:15:05 -04:00 |
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Greg Von Kuster
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064a874217
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Added missing wiki link referred to for eample config settings per Dave & Jen.
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2011-08-17 08:59:56 -04:00 |
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Nate Coraor
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8eff282492
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A missing flush caused the test for whether a dataset could be removed from disk on user purge to always return False.
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2011-08-16 13:03:10 -04:00 |
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Dannon Baker
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efb84f85b5
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Histories API (jdlogicman) and cleanup.
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2011-08-16 12:33:35 -04:00 |
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Nate Coraor
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0335a2677f
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Make nice_size able to display terabytes, and set a default cutoff for users in the user disk usage reports.
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2011-08-16 12:02:34 -04:00 |
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Nate Coraor
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00858eb310
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Reports: Add a per-user disk usage report.
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2011-08-16 10:40:10 -04:00 |
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Greg Von Kuster
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3b1eecd770
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Add the ability for a tool shed admin to browse repository metadata, and implement fixes for setting repository metadata for repositories with multiple tools.
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2011-08-15 16:12:12 -04:00 |
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Nate Coraor
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be78003d4e
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Merged the xml_filetype branch from Peter Cock, which adds a generic XML datatype.
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2011-08-15 13:28:40 -04:00 |
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Nate Coraor
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ab0cf6644f
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Close the xml_filetype branch.
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2011-08-15 13:27:43 -04:00 |
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Greg Von Kuster
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db410b99c4
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Change the bugs_email config setting to be the url to our new support wiki.
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2011-08-15 09:18:52 -04:00 |
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Jeremy Goecks
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08cfd112cd
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(1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool.
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2011-08-14 19:49:26 -04:00 |
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Peter Cock
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29bc117ac1
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Add missing requirement and fix incorrect help text in extract sequence tool
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2011-08-12 10:33:26 +01:00 |
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James Taylor
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8f35ed245f
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Automated merge with https://bitbucket.org/galaxy/galaxy-central
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2011-08-11 18:37:14 -04:00 |
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James Taylor
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2c7b73b7c1
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remove delayed draw and replace with synchronized drawing through requestAnimationFrame (or a fallback)
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2011-08-11 18:36:51 -04:00 |
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Jeremy Goecks
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5b4d3b10ba
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Documentation and white space fixes for Trackster.
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2011-08-11 14:33:15 -04:00 |
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Nate Coraor
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dcad118007
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Very basic "high water mark" per-user job limits.
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2011-08-11 12:49:36 -04:00 |
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Jeremy Goecks
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7169b19f88
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Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny.
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2011-08-11 10:14:53 -04:00 |
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Jeremy Goecks
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92e2f4f48b
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Remove unspecified build validator from extract_genomic_dna tool because it can work with a custom fasta.
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2011-08-11 09:53:14 -04:00 |
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