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:
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- 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
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
Greg Von Kuster
f931001667
Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.
2008-06-30 18:02:53 +00:00
Daniel Blankenberg
86f0862aa4
Move ucsc and gbrowse data from static to tool-data/shared.
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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
Daniel Blankenberg
11a2c767c3
Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.
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MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
2008-05-29 17:38:46 +00:00
Daniel Blankenberg
93ae699b83
Adding a new parameter type drill_down. This parameter type creates a hierarchical set of checkboxes or radiobuttons.
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For a multiple select, checkboxes must be used. When not allowing multiple values, radiobuttons must be used.
Options returned from user selections can either be exact, or recursive (the selection of an upper option will result in the passing of all lower options to the command line).
Options can be filtered based upon a metadata key of an input dataset.
Options can also be loaded from a configuration file that exists outside of the tool's xml file.
If javascript is enabled, option hierarchies are expandable and collapsable.
The annotation profiler has been updated to use this parameter type for table selection. See this tool as an example of use.
2008-05-07 17:10:35 +00:00
Wen-Yu Chung
3f14b0f53a
add restrictions on megablast parameters.
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add new tool wrappers for RMAP and testing data.
add a new location file.
However RMAP is designed for x86_64 machines.
2008-04-18 19:31:57 +00:00
Daniel Blankenberg
7f89a78f35
Add tool for profiling locally cached annotations from the UCSC table browser.
2008-04-09 17:34:35 +00:00
Greg Von Kuster
b4d0ff6cab
Commenting data lines in .loc.sample tool-data files so tools will not throw exceptions.
2008-04-03 14:31:16 +00:00
Wen-Yu Chung
31546f5988
update blastdb.loc sample file.
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use this file to pass functional test.
2008-04-02 20:51:48 +00:00
Wen-Yu Chung
78802fa73b
add scripts for preparing nt and wgs databases.
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update blastdb location file, wgs is available now.
2008-03-27 17:41:40 +00:00
Wen-Yu Chung
3c1037f13b
update blat and megablast wrapper. change blastdb.loc file, now don't need all chunks id.
2008-03-26 16:01:40 +00:00
Greg Von Kuster
cd52cabd48
Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.
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Galaxy developers should execute the following commands in their $UNIVERSE_HOME/tool-data directories:
ln -s /depot/data2/galaxy/alignseq.loc alignseq.loc
ln -s /depot/data2/galaxy/binned_scores.loc binned_scores.loc
ln -s /depot/data2/galaxy/blastdb.loc blastdb.loc
ln -s /depot/data2/galaxy/encode_datasets.loc encode_datasets.loc
ln -s /depot/data2/galaxy/liftOver.loc liftOver.loc
ln -s /depot/data2/galaxy/maf_index.loc maf_index.loc
ln -s /depot/data2/galaxy/maf_pairwise.loc maf_pairwise.loc
ln -s /depot/data2/galaxy/microbes/microbial_data.loc microbial_data.loc
ln -s /depot/data2/galaxy/phastOdds.loc phastOdds.loc
ln -s /depot/data2/galaxy/quality_scores.loc quality_scores.loc
ln -s /depot/data2/galaxy/regions.loc regions.loc
ln -s /depot/data2/galaxy/twobit.loc twobit.loc
2008-03-21 18:31:39 +00:00
Greg Von Kuster
c1c6b7f077
Another locally cached Galaxy data file.
2008-03-20 20:51:23 +00:00
Greg Von Kuster
c0f960fe0c
Missed a sample locally cahced data file, added the Fetch closest feature tool to mains tool config.
2008-03-20 14:44:24 +00:00
Greg Von Kuster
a2ed07169d
Sample locally cached data files used by certain Galaxy tools.
2008-03-20 14:21:01 +00:00
Kelly Vincent