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122 Commits
Author SHA1 Message Date
Dannon Baker ee4f077c52 Per @yhoogstrate's suggestion https://github.com/galaxyproject/galaxy/commit/c0c286a9c69dcb23a50a0b9b249cd6e5b09a3aad#commitcomment-12594774, retab .loc.samples 2015-08-10 20:04:51 -04:00
Daniel Blankenberg 8d2f9f77eb Update modencode dbkeys in gbrowse_build_sites.txt 2015-05-20 12:47:01 -04:00
Daniel Blankenberg c17a9ca15d 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. 2015-03-26 10:47:58 -04:00
Daniel Blankenberg 1260d07a28 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). 2015-02-27 15:50:28 -05:00
Daniel Blankenberg 0ea41e7419 Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running). 2015-02-11 20:39:38 +00:00
Lance Parsons f77324d3a3 Removed blastdb_p.loc.sample, moved to tool-shed repo 2014-12-10 12:43:33 -05:00
Nate Coraor 4227d0eabb Remove additional pieces from old genome index system. 2014-07-27 02:48:40 -04:00
Dave Bouvier a3018feb02 Migrate 22 tools from the distribution to the tool shed. 2014-05-19 13:01:46 -04:00
Dave Bouvier 83af05b1f2 Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation. 2014-04-01 11:04:32 -04:00
Nate Coraor 794484e8c3 Rename ucsc_build_sites.txt to .sample. 2014-02-27 16:37:48 -05:00
Nate Coraor 9c64fc123e Remove broken and/or obsolete tools. 2014-01-27 13:58:31 -05:00
Dave Bouvier 448d9f55eb Migrate 43 tools from the distribution to the tool shed. 2014-01-27 09:53:14 -05:00
Ross Lazarus 93c3148b4c backout -r 10811 2013-10-08 10:56:03 +11:00
Ross Lazarus 66b690d599 backout -r 10802 2013-10-08 10:53:45 +11:00
Ross Lazarus 59bd638b82 updated ucsc builds 2013-10-07 10:41:50 +11:00
Ross Lazarus 87b1203b4a branch merge 2013-10-05 09:56:05 +10:00
Dave Bouvier 962be8d8ec Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories. 2013-10-01 15:49:08 -04:00
Dannon Baker 9544149163 Include hg19 in ucsc_build_sites.txt 2013-09-19 09:59:49 -04:00
Ross Lazarus 652fec3488 monkeypatches to output.py 2013-08-07 09:45:35 +10:00
Nate Coraor 812aebdd62 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. 2013-07-30 12:44:05 -04:00
Nicola Soranzo 70996cfb3d Add new loc file for SAMtools indexes to support genome variants 2013-04-18 19:25:55 +02:00
Jeremy Goecks 6b1165be53 Improved documentation in bowtie2 loc file. 2013-02-13 11:04:54 -05:00
James Taylor a4318d4817 genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility 2013-02-03 23:21:17 -05:00
Dave Bouvier 917d5a72e8 Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process. 2012-11-26 10:18:47 -05:00
Dave Bouvier c2eeee7b9f Migrate BWA to the tool shed. 2012-09-28 15:35:44 -04:00
Daniel Blankenberg bb15315fed Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites. 2012-08-22 12:35:23 -04:00
Dave Bouvier 36dbacf8f1 Cleaned up code, added searchable list of NCBI builds. 2012-07-05 09:56:54 -04:00
Dave Bouvier 33a50cd7ee Also added missing publicbuilds.txt 2012-06-26 15:18:19 -04:00
Dave Bouvier 8096e294a6 Added missing builds.txt for Ensembl, fixed erroneous first line in output. 2012-06-26 15:10:25 -04:00
Jeremy Goecks 7c40df458e Skeleton wrapper for Bowtie2. 2012-04-26 15:28:17 -04:00
Richard Burhans 30c6ec3fbe remove Genome Diversity {test,tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository 2012-04-09 16:34:51 -04:00
Dannon Baker c0c286a9c6 Convert loc file examples to use tabs instead of spaces. 2012-03-23 08:59:34 -04:00
Dannon Baker 7ff0131d81 =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample 2012-03-23 08:24:42 -04:00
Guruprasad Anada 1e51b17b80 Added apiMel3 to manual builds. 2012-02-23 13:38:01 -05:00
Daniel Blankenberg 11fd8d08e4 Add RViewer external display application. 2012-02-17 10:00:42 -05:00
Guruprasad Anada d487d10518 added cacao genome to manual builds 2012-01-30 12:29:39 -05:00
Daniel Blankenberg d8755293e3 GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file. 2011-12-05 12:27:54 -05:00
Richard Burhans a3f8cb2efc python version of "phyloP interspecies conservation scores" tool 2011-11-30 12:05:59 -05:00
Daniel Blankenberg 09bcf6e95a Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix). 2011-11-15 17:24:38 -05:00
Daniel Blankenberg d09305f56b Update annotation profiler tool sample configuration file. 2011-07-07 12:13:49 -04:00
Ross Lazarus d53c3e984f Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository 
This is a backout of commit 5765
 2011-07-06 09:44:56 +10:00
Ross Lazarus 86b55bb0c0 branch merge 2011-07-05 12:40:43 +10:00
Kelly Vincent 53471e1615 Added new builds to manual builds list 2011-06-24 16:13:48 -04:00
Kelly Vincent 08dc13008e Added builds and length info to manual builds list 2011-06-10 16:31:52 -04:00
Kelly Vincent acb1fbc6f0 Added hg_g1k_v37 to manual builds 2011-05-19 15:38:12 -04:00
Nate Coraor a7f17d327d Add a method to add manual builds to buildbot runs. 2011-05-12 11:53:32 -04:00
Kelly Vincent 0354a3f661 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 2011-04-22 15:09:45 -04:00
Richard Burhans d3b7aaeb6b initial version of Webb's genome diversity tools 2011-04-21 17:22:27 -04:00
Daniel Blankenberg daf645f53a Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c. 2011-04-07 08:39:07 -04:00
Kelly Vincent d969f29c01 Corrected typo in manual build name 2011-04-06 10:16:30 -04:00