John Chilton
34e1273f9b
Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS.
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As discussed here https://bitbucket.org/galaxy/galaxy-central/pull-request/489/srma-tool-requires-at-least-2048m-memory/diff . Thanks to Bjoern for input.
2014-09-22 13:20:49 -04:00
Lance Parsons
0a3e5d274f
SRMA tool requires at least 2048m memory and LENIENT validation stringency
2014-09-04 16:12:51 -04:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Nicola Soranzo
62673b0134
Fix for failure preparing job: "NotFound: cannot find 'mfl'" with paired-end library.
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Add mate FASTQ file to inputs.
'ls' param was not used.
Add missing '-mfl ' to MosaikBuild command.
Remove always empty $lm variable.
Add <version_command>.
2013-12-06 11:20:56 +01:00
Nicola Soranzo
926d6de51d
Specify mosaik v. 1.1.0021 (last compatible with the wrapper). Add requirement for samtools.
2013-12-06 11:17:25 +01:00
Nicola Soranzo
3e528ae02b
Enhance bowtie2 to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:53:52 +01:00
Nicola Soranzo
c4e9999a33
Enhance mosaik to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:53:35 +01:00
John Chilton
162e4de0e1
Enhance bfast to utilize GALAXY_SLOTS configuration when available.
2013-11-05 13:46:06 -06:00
John Chilton
60488bf064
Merged in nsoranzo/galaxy-central-tools2 (pull request #234 )
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Bug fixes for 3 tools (rebased #222 )
2013-10-16 12:49:34 -05:00
Aysam Guerler
d9b284bf5e
Modify bowtie error handler
2013-10-16 11:03:51 -04:00
Ross Lazarus
c1af859f90
revert bowtie2 and tophat2 wrappers
2013-10-08 13:34:54 +11:00
Ross Lazarus
4caf74eaa6
backout -r 10806
2013-10-08 10:54:45 +11:00
Ross Lazarus
070ee188fa
backout -r 10800
2013-10-08 10:52:21 +11:00
Ross Lazarus
a17e071f38
hg backout -r 1092b0d
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backout unintended commits to tophat and bowtie2 wrappers
2013-10-08 10:24:59 +11:00
Nicola Soranzo
f109dea17f
Fix for "syntax error near unexpected token `;;'".
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<command> should not end with a semicolon, otherwise
BaseJobRunner.build_command_line() would create a bash command containing
';;' when appending metadata setting commands.
2013-10-04 18:15:22 +02:00
Ross Lazarus
7146ba9c38
tweaks. ready for branch merge
2013-08-12 13:04:57 +10:00
Ross Lazarus
a4622551de
branch merge with central
2013-08-08 15:38:10 +10:00
Aysam Guerler
59dea4d61f
Bowtie2: Added quotation marks to group selection and added basic tool test
2013-08-07 14:17:43 -04:00
Ross Lazarus
8604c3b542
fixing on_string again. Add job title to tophat2
2013-08-05 10:27:13 +10:00
Ross Lazarus
24dd794183
update bowtie2 wrapper
2013-08-04 17:44:45 +10:00
Aysam Guerler
fe048358fd
bowtie2 wrapper update
2013-07-19 14:56:39 -04:00
Aysam Guerler
3367d43d49
bowtie2 tool wrapper update
2013-07-19 14:30:38 -04:00
Jeremy Goecks
7538091308
Change order of Bowtie2 output datasets to put aligned reads at top of history.
2013-01-30 12:55:49 -05:00
Andrea Sbardellati
47630c9ed6
Add option for writing not aligned reads to file
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Reviewed-by: Nicola Soranzo <soranzo@crs4.it >
2013-01-18 17:11:04 +01:00
Nicola Soranzo
b571178cc8
Add missing samtools requirement to bowtie2 wrapper
2013-01-10 18:50:51 +01:00
Jeremy Goecks
d254249fda
Fix bug in bowtie2 wrapper that prevented wrapper from working with old versions of samtools.
2013-01-08 09:25:16 -05:00
Jeremy Goecks
b9ed8bec42
Bowtie2 wrapper: move read group parameters out of full parameter settings and into own group.
2012-12-18 13:35:56 -05:00
Jeremy Goecks
1149f1fcf3
Add simple read group options for Bowtie2.
2012-12-18 12:08:47 -05:00
Dave Bouvier
917d5a72e8
Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
2012-11-26 10:18:47 -05:00
Dave Bouvier
6a44e8f34a
Remove the bwa wrappers from the repository.
2012-10-01 09:24:33 -04:00
Jeremy Goecks
41682ee6c9
Output sorted BAM from Bowtie2.
2012-08-22 16:49:12 -04:00
Jeremy Goecks
6f2c3d6761
Have Bowtie2 wrapper produce BAM rather than SAM output.
2012-06-11 15:52:36 -04:00
Jeremy Goecks
0c12da85ba
Add min, max insert size parameters to bowtie2 wrapper.
2012-06-08 14:03:41 -04:00
Jeremy Goecks
a08c0c03ce
Fix bug in setting Bowtie2 parameters.
2012-06-08 13:48:37 -04:00
Jeremy Goecks
63fec8c332
Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.
2012-06-06 15:27:59 -04:00
Jeremy Goecks
7c40df458e
Skeleton wrapper for Bowtie2.
2012-04-26 15:28:17 -04:00
Daniel Blankenberg
0372d1fe06
Fix for BWA -R option.
2012-04-10 09:24:25 -04:00
Daniel Blankenberg
8a6b0001c2
Minor fix for 04e8ed0cd930.
2011-11-29 17:35:14 -05:00
Daniel Blankenberg
023c4db69e
Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
2011-11-29 17:30:14 -05:00
Daniel Blankenberg
8b402babb2
Update SRMA wrapper to use data tables.
2011-10-31 09:49:51 -04:00
Jennifer Jackson
2ff5dcfb33
Other genome description: corrected typo.
2011-10-10 18:42:31 -04:00
Jennifer Jackson
a1d4bb9bab
Other genome description: revised all, corrected canonical male
2011-10-10 18:33:48 -04:00
Daniel Blankenberg
591ee9a922
Import patch contributed by Assaf Gordon allowing bwa_wrapper to work directly on fastqillumina formatted files. Closes #635 .
2011-08-08 09:35:48 -04:00
Daniel Blankenberg
33c4c0d4eb
Make setting read groups in BWA off by default.
2011-08-04 13:30:01 -04:00
Kelly Vincent
c565726192
Updated help section of BWA wrappers to include tags for the RG header record type
2011-05-12 13:38:00 -04:00
Kelly Vincent
9eaf2ec821
Updated SRMA to properly set dbkey and changed functional tests so that they can handle a single line difference for the SRMA version number tag
2011-05-11 10:49:32 -04:00
Kelly Vincent
78a4a14131
BWA enhancements: added new options to support v. 0.5.9 (-n and -r for samse/sampe and -N for sampe only); fixed dbkey setting; set Sam header suppression off by default
2011-05-09 16:37:13 -04:00
Kelly Vincent
0017486eaa
Sam header suppression made optional in BFAST and default set to off for BFAST and Bowtie. Fixed dbkey setting on outputs for for BFAST, Bowtie, Mosaik. Fixed sorting of built-in builds for these tools so ordered by pretty name.
2011-05-09 12:11:54 -04:00
Nate Coraor
1fdfacc977
Set the ftype of SRMA test outputs so the BAMs are compared as SAMs
2011-03-23 10:59:26 -04:00
Kelly Vincent
a4f910c730
Update SRMA test files so that functional tests pass
2011-03-08 16:17:09 -05:00
John Chilton