Nolan Woods
b7e1238c6b
Remove redundant default build
2020-11-09 14:35:21 -08:00
Nicola Soranzo
926f0abde2
Update UCSC builds
2018-08-22 15:24:25 +01:00
Björn Grüning
cac9c980df
remove obsolete line
2017-04-07 17:13:56 +02:00
Bjoern Gruening
ab1f7eae4d
synchronise against latest UCSC versions
2017-04-05 15:17:57 +02:00
Daniel Blankenberg
04b7d11f05
Add hg38 to main for ucsc_build_sites.txt.sample
2016-07-27 12:16:21 -04:00
Lance Parsons
5810a853b0
Move manual_builds.txt to manual_builds.txt.sample to allow for customization
2015-08-18 14:00:30 -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
Nate Coraor
4227d0eabb
Remove additional pieces from old genome index system.
2014-07-27 02:48:40 -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
Ross Lazarus
93c3148b4c
backout -r 10811
2013-10-08 10:56:03 +11:00
Ross Lazarus
59bd638b82
updated ucsc builds
2013-10-07 10:41:50 +11:00
Dannon Baker
9544149163
Include hg19 in ucsc_build_sites.txt
2013-09-19 09:59:49 -04:00
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
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
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
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
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
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
Kelly Vincent
d3d26a7149
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
2011-03-29 13:59:07 -04:00
Daniel Blankenberg
7ab9f182dc
Add SGD Yeast genome Gbrowse display site.
2011-03-23 09:03:13 -04:00
Kelly Vincent
833478bbbd
Added two more builds to the manual builds list
2011-03-10 16:08:39 -05:00
Kelly Vincent
b5ee9ee8c7
Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds
2011-03-10 13:28:33 -05:00
Kelly Vincent
7004393599
Adding several genomes to the manual builds list
2011-02-09 12:36:40 -05:00
Brad Chapman
8679ac8442
Add support for displaying BAM files at Ensembl
2010-10-06 11:03:28 -04:00
Kelly Vincent
1bd873020b
Added Sscrofa9.58 to manual_builds.txt and removed phiX from builds.txt.sample (it's in manual_builds.txt)
2010-07-15 12:04:49 -04:00
Nate Coraor
7ffcc6184b
Make the PSU BX browser a UCSC browser instead of being a different display type.
2010-06-29 12:40:42 -04:00
Daniel Blankenberg
ab53cc6d3b
First pass at adding Ensembl browsers as an external display application. Two different URL generation and data attachment methods are used; one for 'old' Ensembl archives older than ~November 2008 and another for Ensembl sites using the current method. The tool-data/shared/ensembl/ensembl_sites.txt file contains the site and build information for using the current method; the tool-data/shared/ensembl/ensembl_sites_data_URL.txt file has the site and build information for when the older method is to be used.
...
The new method follows: http://www.ensembl.org/info/docs/webcode/linking.html
The old method follows: http://aug2007.archive.ensembl.org/Homo_sapiens/helpview?se=1;kw=urlsource
2010-05-21 15:25:56 -04:00
Greg Von Kuster
3eef17415b
Fixes for displaying appropriate datasets in GBrowse wormbase, modENCODE worm, and modENCODE fly.
2010-05-12 14:37:00 -04:00
Nate Coraor
2bd25bf652
Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one
2010-05-10 12:50:09 -04:00
Kelly Vincent
dbfa0a7cca
Updated builds.txt (and manual_builds.txt) to newest version, corresponding to that on main. Includes hg19 and phiX correction.
2010-05-06 12:11:47 -04:00
Daniel Blankenberg
5ede7cba83
Display Application framework enhancements.
...
Add the ability for display applications to be populated dynamically based upon the content of (e.g. tabular) files.
Display application links can be filtered by various attributes, including e.g. dataset dbkey matching from field in a file or an attribute matching a Galaxy application configuration setting.
Param and Data URL values can now be generated dynamically, allowing e.g unique base filenames to be created and used.
See updated xml configurations in /display_applications/ for examples of syntax.
2010-03-11 14:35:36 -05:00
Guruprasad Anada
4d0183412f
Converted space to tab on mm5 declaration line in manual_builds.txt.
2010-03-04 13:02:56 -05:00
Kelly Vincent
7403f4301b
Updated Bowtie wrapper for new fastqcssanger datatype, and added equCab2 to builds.txt so sam_to_bam and sam_pileup will pass
2010-03-03 15:37:43 -05:00
Guruprasad Anada
20bb7f6d5b
Added mm5 to the list of manual builds
2010-02-18 11:26:39 -05:00
Greg Von Kuster
90be3f67c0
Add the bx browser as a display app for builds hg18,hg19.mm8.mm9, and add the bx browser to the tool config for main.
2010-02-17 12:45:32 -05:00
Nolan Woods