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
Nate Coraor
607d670872
Add Genetrack tools and display site
2009-11-06 14:22:44 -05:00
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
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
Greg Von Kuster
fb2441caa1
merging heads
2009-03-26 11:13:13 -04:00
Greg Von Kuster
bd41001a99
i18n fix: dataset.info should not be translated since it will generally not have an entry in the catalog. Wormbase fixes: URL to main site corrected, and all supported builds added to gbrowse_build_sites.txt.
2009-03-26 09:34:05 -04:00
Daniel Blankenberg
201146e4a2
Adding phiX to manual_builds.txt.
2009-03-16 11:39:59 -04:00
Greg Von Kuster
162d0ce00f
Fix gbrowse display links
2009-01-30 15:52:12 -05:00
Daniel Blankenberg
86f0862aa4
Move ucsc and gbrowse data from static to tool-data/shared.
...
Cron scripts on test and main will need to be updated when the server is.
GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
2008-06-03 18:53:26 +00:00
Kelly Vincent