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4,839 Commits 63 Branches 243 Tags
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22 Commits
Author SHA1 Message Date
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