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
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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
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
Daniel Blankenberg
a01df218d7
Update CCAT to version 3.0.
2011-03-16 10:41:38 -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
Dannon Baker
668d03ba7d
Initial commit of Mosaik and Freebayes.
2011-02-23 14:01:58 -05:00
Kelly Vincent
7004393599
Adding several genomes to the manual builds list
2011-02-09 12:36:40 -05:00
Kelly Vincent
76b3cb5844
Added BWA color space wrapper; fixed names of FASTQ test files to indicate data type
2011-01-12 12:13:54 -05:00
Daniel Blankenberg
b9d790af55
Add CCAT ChIP-seq peak/region caller.
2011-01-03 11:15:29 -05:00
Kelly Vincent
6f78ce7081
Fixed inconsistency in PerM loc.sample files
2010-11-17 11:43:40 -05:00
Kelly Vincent
a0a1f44c32
Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory.
2010-11-08 00:43:02 -05:00
Kelly Vincent
7d0ff14df9
Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.
2010-11-08 00:10:13 -05:00
Kelly Vincent
c75adfdda5
Adding NGS simulation tool
2010-11-03 13:52:52 -04:00
Peter Cock
7c69382bbc
Introduce blastdb_p.loc for protein BLAST databases
2010-09-21 17:05:24 +01:00
Peter Cock
4a013963b2
Update comments in blastdb.loc.sample for intended usage
2010-09-21 17:01:19 +01:00
Brad Chapman
8679ac8442
Add support for displaying BAM files at Ensembl
2010-10-06 11:03:28 -04:00
Richard Burhans
641cc2318c
Fixed sample .loc file for FunDO tool
2010-09-16 15:29:51 -04:00
Richard Burhans
e6a05f3bd1
Updates to disease ontology and lps tools
2010-09-15 12:21:37 -04:00
Richard Burhans
c4ef1f8b5b
Initial checkin of Human Genome Variation tools
2010-09-14 18:20:15 -04:00
Kelly Vincent
f6a3996d9b
Adding SRMA wrapper and all associated test files and index loc sample
2010-08-19 18:17:31 -04:00
Daniel Blankenberg
94c7417f37
Add BFAST Mapper tool and wrapper.
2010-08-18 16:52:06 -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.
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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
Ross Lazarus
afec1f9c3a
SNP/WGA tool changes only
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Updates to functional test outputs
Minor tweaks to some tests
All now pass when run using -sid but there's something busted when a full functional test is run
2010-05-10 10:17:11 -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
fdef6331e5
Updates for 'Profile Annotations for a set of genomic intervals' tool. This tool will now report a 'data version'. Add a script that creates the indexes and table description xml from a UCSC database dump.
2010-04-23 11:14:26 -04:00
Jeremy Goecks
b1606f670c
Rudimentary Cufflinks wrapper. Also created directory for all NGS RNA-seq tools, and Tophat now uses Bowtie indices rather than own indices file.
2010-04-13 17:12:00 -04:00
Jeremy Goecks
a96456a0c5
Add Tophat tool. Components: a wrapper script, indicecs file, test data, and functional test. It may be useful to have a single indices file for both Tophat and Bowtie because Tophat uses Bowtie.
2010-03-31 17:46:25 -04:00
Greg Von Kuster
47463daa73
Add the add_scores tool.
2010-03-23 15:43:58 -04:00
Greg Von Kuster
f129f97f27
Add the codingSnps tool.
2010-03-23 13:53:21 -04:00
Kelly Vincent
fc8a137b5e
First pass as PerM. Also made cosmetic changes to BWA.
2010-03-17 16:40:36 -04:00
Daniel Blankenberg