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.
...
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
...
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
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
Kelly Vincent
b5dab3a63f
Removed SOLiD option from BWA, cleaned up Bowtie and BWA wrapper interfaces, and changed name of BWA index loc file
2010-01-22 10:49:38 -05:00
Kelly Vincent
b5fa090092
Added SOLiD (colorspace) support to Bowtie wrapper tool
2010-01-11 17:04:45 -05:00
Kelly Vincent
ebc67a6bc7
Updated megablast_wrapper tool to allow for date to be included with database name and displayed (so user knows how current it is)
2009-12-09 18:50:12 -05:00
Greg Von Kuster
81bd968bd1
Fixes for lastz_wrapper that includes job splitting, more functional tests, removed incorrectly committed .loc file and committed the .loc.sample file.
2009-12-01 20:16:41 -05:00
Greg Von Kuster
20628e8381
First pass of the lastz tool wrapper that includes job splitting - works but needs polishing.
2009-11-27 10:53:50 -05:00
Nate Coraor
607d670872
Add Genetrack tools and display site
2009-11-06 14:22:44 -05:00
Kelly Vincent
c2d26c9a7c
Updated several sample index loc files to make it clearer how the actual loc files should appear
2009-10-07 15:31:18 -04:00
Greg Von Kuster
f0fd5a25e7
Add Arabidopsis integration at TAIR and UCLA patch provided by Brad Chapman ( handles # 135 ).
2009-10-07 11:12:39 -04:00
Greg Von Kuster
de1ea7ae0a
Eliminate the use of the genetrack controller, merge the template code for uploading library datasets, and several bug fixes:
...
- The genetrack controller is no longer used ( I'll delete it soon ), so the GeneTrack application is now loosely coupled
- Merge the 2 new_dataset.mako templates into one common code module name library_dataset_common.mako
- Rename all of the library upload form fields to have the same names as the history upload form fields
- Eliminate a 2nd runtool_btn from being rendered on the same form in tool_form.mako
- Fix bug and add functional tests to cover uploading a library dataset that does not include a template
2009-09-22 14:04:48 -04:00
Guruprasad Anada
7a978e7ce8
Updating FASTX tool-set to the latest version v0.0.10
2009-09-14 17:03:17 -04:00
Kelly Vincent
e13eaf8a0c
Added Bowtie wrapper tool
2009-09-11 14:38:05 -04:00
Guruprasad Anada
8b193b63fd
Updated manual builds will L. major (2005) genome.
2009-09-10 10:42:50 -04:00
Guruprasad Anada
c689c32831
Updated manual builds list with human herpesvirus genome.
2009-09-09 11:01:22 -04:00
Kelly Vincent
9d0dd5f7ce
Added samtools-based tools (sam_to_bam, sam_merge, sam_pileup) with their supporting files and modified Bam datatype so temp files are properly cleaned up
2009-08-28 15:59:16 -04:00
Kelly Vincent
b6ea9ed1eb
Added BWA wrapper tool to Short Read Mapping Tools
2009-07-24 15:13:11 -04:00
Greg Von Kuster
fb2441caa1
merging heads
2009-03-26 11:13:13 -04:00
Dannon Baker