 Nate Coraor
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9c64fc123e
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Remove broken and/or obsolete tools.
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2014-01-27 13:58:31 -05:00 |
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Dave Bouvier
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448d9f55eb
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Migrate 43 tools from the distribution to the tool shed.
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2014-01-27 09:53:14 -05:00 |
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Ross Lazarus
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93c3148b4c
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backout -r 10811
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2013-10-08 10:56:03 +11:00 |
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Ross Lazarus
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66b690d599
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backout -r 10802
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2013-10-08 10:53:45 +11:00 |
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Ross Lazarus
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59bd638b82
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updated ucsc builds
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2013-10-07 10:41:50 +11:00 |
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Ross Lazarus
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87b1203b4a
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branch merge
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2013-10-05 09:56:05 +10:00 |
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Dave Bouvier
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962be8d8ec
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Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.
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2013-10-01 15:49:08 -04:00 |
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Dannon Baker
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9544149163
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Include hg19 in ucsc_build_sites.txt
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2013-09-19 09:59:49 -04:00 |
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Ross Lazarus
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652fec3488
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monkeypatches to output.py
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2013-08-07 09:45:35 +10:00 |
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Nate Coraor
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812aebdd62
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Backout af20b15f7eda, these changes will be reapplied after tools using the sam_fa_indices data table have been migrated to the Tool Shed in their original state and updated to use the new table format.
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2013-07-30 12:44:05 -04:00 |
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Nicola Soranzo
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70996cfb3d
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Add new loc file for SAMtools indexes to support genome variants
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2013-04-18 19:25:55 +02:00 |
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Jeremy Goecks
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6b1165be53
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Improved documentation in bowtie2 loc file.
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2013-02-13 11:04:54 -05:00 |
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James Taylor
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a4318d4817
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genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility
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2013-02-03 23:21:17 -05:00 |
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Dave Bouvier
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917d5a72e8
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Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
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2012-11-26 10:18:47 -05:00 |
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Dave Bouvier
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c2eeee7b9f
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Migrate BWA to the tool shed.
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2012-09-28 15:35:44 -04:00 |
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Daniel Blankenberg
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bb15315fed
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Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites.
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2012-08-22 12:35:23 -04:00 |
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Dave Bouvier
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36dbacf8f1
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Cleaned up code, added searchable list of NCBI builds.
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2012-07-05 09:56:54 -04:00 |
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Dave Bouvier
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33a50cd7ee
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Also added missing publicbuilds.txt
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2012-06-26 15:18:19 -04:00 |
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Dave Bouvier
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8096e294a6
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Added missing builds.txt for Ensembl, fixed erroneous first line in output.
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2012-06-26 15:10:25 -04:00 |
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Jeremy Goecks
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7c40df458e
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Skeleton wrapper for Bowtie2.
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2012-04-26 15:28:17 -04:00 |
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Richard Burhans
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30c6ec3fbe
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remove Genome Diversity {test,tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository
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2012-04-09 16:34:51 -04:00 |
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Dannon Baker
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c0c286a9c6
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Convert loc file examples to use tabs instead of spaces.
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2012-03-23 08:59:34 -04:00 |
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Dannon Baker
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7ff0131d81
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=Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample
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2012-03-23 08:24:42 -04:00 |
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Guruprasad Anada
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1e51b17b80
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Added apiMel3 to manual builds.
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2012-02-23 13:38:01 -05:00 |
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Daniel Blankenberg
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11fd8d08e4
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Add RViewer external display application.
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2012-02-17 10:00:42 -05:00 |
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Guruprasad Anada
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d487d10518
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added cacao genome to manual builds
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2012-01-30 12:29:39 -05:00 |
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Daniel Blankenberg
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d8755293e3
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GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file.
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2011-12-05 12:27:54 -05:00 |
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Richard Burhans
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a3f8cb2efc
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python version of "phyloP interspecies conservation scores" tool
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2011-11-30 12:05:59 -05:00 |
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Daniel Blankenberg
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09bcf6e95a
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Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).
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2011-11-15 17:24:38 -05:00 |
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Daniel Blankenberg
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d09305f56b
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Update annotation profiler tool sample configuration file.
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2011-07-07 12:13:49 -04:00 |
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Ross Lazarus
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d53c3e984f
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Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
This is a backout of commit 5765
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2011-07-06 09:44:56 +10:00 |
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Ross Lazarus
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86b55bb0c0
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branch merge
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2011-07-05 12:40:43 +10:00 |
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Kelly Vincent
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53471e1615
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Added new builds to manual builds list
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2011-06-24 16:13:48 -04:00 |
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Kelly Vincent
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08dc13008e
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Added builds and length info to manual builds list
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2011-06-10 16:31:52 -04:00 |
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Kelly Vincent
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acb1fbc6f0
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Added hg_g1k_v37 to manual builds
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2011-05-19 15:38:12 -04:00 |
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Nate Coraor
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a7f17d327d
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Add a method to add manual builds to buildbot runs.
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2011-05-12 11:53:32 -04:00 |
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Kelly Vincent
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0354a3f661
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Added picard_index.loc.sample file and changed data tables so that both picard and srma tools look in picard_index.loc instead of srma_index.loc
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2011-04-22 15:09:45 -04:00 |
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Richard Burhans
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d3b7aaeb6b
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initial version of Webb's genome diversity tools
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2011-04-21 17:22:27 -04:00 |
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Daniel Blankenberg
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daf645f53a
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Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
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2011-04-07 08:39:07 -04:00 |
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Kelly Vincent
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d969f29c01
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Corrected typo in manual build name
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2011-04-06 10:16:30 -04:00 |
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Kelly Vincent
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d3d26a7149
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Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds
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2011-03-29 13:59:07 -04:00 |
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Daniel Blankenberg
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7ab9f182dc
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Add SGD Yeast genome Gbrowse display site.
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2011-03-23 09:03:13 -04:00 |
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Daniel Blankenberg
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a01df218d7
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Update CCAT to version 3.0.
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2011-03-16 10:41:38 -04:00 |
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Kelly Vincent
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833478bbbd
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Added two more builds to the manual builds list
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2011-03-10 16:08:39 -05:00 |
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Kelly Vincent
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b5ee9ee8c7
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Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds
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2011-03-10 13:28:33 -05:00 |
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Dannon Baker
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668d03ba7d
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Initial commit of Mosaik and Freebayes.
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2011-02-23 14:01:58 -05:00 |
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Kelly Vincent
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7004393599
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Adding several genomes to the manual builds list
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2011-02-09 12:36:40 -05:00 |
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Kelly Vincent
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76b3cb5844
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Added BWA color space wrapper; fixed names of FASTQ test files to indicate data type
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2011-01-12 12:13:54 -05:00 |
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Daniel Blankenberg
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b9d790af55
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Add CCAT ChIP-seq peak/region caller.
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2011-01-03 11:15:29 -05:00 |
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Kelly Vincent
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6f78ce7081
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Fixed inconsistency in PerM loc.sample files
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2010-11-17 11:43:40 -05:00 |
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