 Daniel Blankenberg
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9091acc690
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Update q2view_display.loc.sample
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2022-07-05 09:43:29 -07:00 |
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Daniel Blankenberg
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797d63a01f
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Add q2view display application.
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2022-07-05 09:43:29 -07:00 |
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Nolan Woods
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b7e1238c6b
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Remove redundant default build
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2020-11-09 14:35:21 -08:00 |
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Daniel Blankenberg
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dfb5a988e4
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Add GEDA for iCn3D
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2019-07-17 09:54:43 -04:00 |
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Daniel Blankenberg
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428c6632f0
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Remove errant space in intermine_simple_display.loc.sample
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2019-02-04 14:32:02 -05:00 |
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Nicola Soranzo
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926f0abde2
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Update UCSC builds
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2018-08-22 15:24:25 +01:00 |
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Daniel Blankenberg
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58c68d408f
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add missing intermine_simple_display.loc.sample
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2018-07-06 09:16:58 -04:00 |
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Björn Grüning
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cac9c980df
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remove obsolete line
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2017-04-07 17:13:56 +02:00 |
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Bjoern Gruening
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ab1f7eae4d
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synchronise against latest UCSC versions
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2017-04-05 15:17:57 +02:00 |
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peterjc
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2956f94aa0
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BLAST database *.loc.sample files
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2016-11-04 17:00:13 +00:00 |
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Daniel Blankenberg
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04b7d11f05
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Add hg38 to main for ucsc_build_sites.txt.sample
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2016-07-27 12:16:21 -04:00 |
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Daniel Blankenberg
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55074c8f33
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Add Phinch as an external display application. Currently linking to a personal copy of Phinch, since it requires https://github.com/PitchInteractiveInc/Phinch/pull/54
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2016-04-01 15:38:53 -04:00 |
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Daniel Blankenberg
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e6bb45b29a
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typo
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2016-03-15 14:09:51 -04:00 |
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Daniel Blankenberg
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0c57453c96
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Add vcf.iobio as a display application.
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2016-03-15 12:57:47 -04:00 |
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Daniel Blankenberg
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46728c5728
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Add bam.iobio as a display application.
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2016-03-15 12:56:54 -04:00 |
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Dannon Baker
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7f3ee5b167
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Merge pull request #612 from lparsons/manual_builds
Move manual_builds.txt to manual_builds.txt.sample
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2015-09-24 17:10:49 -04:00 |
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Lance Parsons
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5810a853b0
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Move manual_builds.txt to manual_builds.txt.sample to allow for customization
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2015-08-18 14:00:30 -04:00 |
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Lance Parsons
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aceb822470
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Remove fastx_clipper_sequences.txt, moved to toolshed
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2015-08-18 13:47:25 -04:00 |
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Dannon Baker
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ee4f077c52
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Per @yhoogstrate's suggestion https://github.com/galaxyproject/galaxy/commit/c0c286a9c69dcb23a50a0b9b249cd6e5b09a3aad#commitcomment-12594774, retab .loc.samples
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2015-08-10 20:04:51 -04:00 |
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Daniel Blankenberg
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8d2f9f77eb
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Update modencode dbkeys in gbrowse_build_sites.txt
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2015-05-20 12:47:01 -04:00 |
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Daniel Blankenberg
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c17a9ca15d
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Re-enable IGV local external display application by default. Add hg38 as available genome. We should probably update this view to either allow any genome or to function like the current web_link_main.
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2015-03-26 10:47:58 -04:00 |
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Daniel Blankenberg
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1260d07a28
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Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).
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2015-02-27 15:50:28 -05:00 |
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Daniel Blankenberg
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0ea41e7419
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Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running).
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2015-02-11 20:39:38 +00:00 |
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Lance Parsons
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f77324d3a3
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Removed blastdb_p.loc.sample, moved to tool-shed repo
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2014-12-10 12:43:33 -05:00 |
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Nate Coraor
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4227d0eabb
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Remove additional pieces from old genome index system.
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2014-07-27 02:48:40 -04:00 |
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Dave Bouvier
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a3018feb02
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Migrate 22 tools from the distribution to the tool shed.
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2014-05-19 13:01:46 -04:00 |
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Dave Bouvier
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83af05b1f2
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Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
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2014-04-01 11:04:32 -04:00 |
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Nate Coraor
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794484e8c3
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Rename ucsc_build_sites.txt to .sample.
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2014-02-27 16:37:48 -05:00 |
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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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