| Tue, 19 Feb 2013 20:59:51 -0600 |
Jim Johnson |
Temporarily use my own copy of samtools until cross dependency support is in release
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| Mon, 18 Feb 2013 15:48:46 -0600 |
Jim Johnson |
Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
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| Mon, 18 Feb 2013 11:17:32 -0600 |
Jim Johnson |
Use repository dependency for samtools with corrected revision
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| Mon, 18 Feb 2013 11:13:47 -0600 |
Jim Johnson |
Use repository dependency for samtools (from main toolshed)
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| Mon, 18 Feb 2013 11:01:18 -0600 |
Jim Johnson |
Use repository dependency for samtools
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| Fri, 28 Dec 2012 14:15:14 -0600 |
Jim Johnson |
Add BQSR and plot_pdf_file options to base_recalibrator.xml
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| Fri, 28 Dec 2012 12:34:05 -0600 |
Jim Johnson |
Replace covariate DinucCovariate with ContextCovariate
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| Fri, 28 Dec 2012 12:08:47 -0600 |
Jim Johnson |
Remove thread options from base_recalibrator.xml
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| Fri, 28 Dec 2012 11:50:20 -0600 |
Jim Johnson |
Fix base_recalibrator.xml option: no_standard_covs
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| Fri, 28 Dec 2012 11:21:40 -0600 |
Jim Johnson |
remove thread options from indel_realigner.xml
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| Fri, 28 Dec 2012 11:08:23 -0600 |
Jim Johnson |
remove thread options from realigner_target_creator.xml
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| Thu, 20 Dec 2012 11:01:55 -0600 |
Jim Johnson |
Update tool_dependencies to GATK v 2.3
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| Thu, 15 Nov 2012 10:18:55 -0600 |
Jim Johnson |
Many fixes to haplotype_caller
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| Thu, 15 Nov 2012 10:18:27 -0600 |
Jim Johnson |
base_recalibrator out_puts gatk_report
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| Thu, 15 Nov 2012 10:17:22 -0600 |
Jim Johnson |
Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2
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| Thu, 08 Nov 2012 13:09:56 -0600 |
Jim Johnson |
Remove unneeded params
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| Thu, 08 Nov 2012 11:50:01 -0600 |
Jim Johnson |
Fix output filters
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| Thu, 08 Nov 2012 10:55:32 -0600 |
Jim Johnson |
Add help to HaplotypeCaller
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| Thu, 08 Nov 2012 10:38:18 -0600 |
Jim Johnson |
Add HaplotypeCaller
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| Tue, 06 Nov 2012 12:07:36 -0600 |
Jim Johnson |
Comment out site options from reduce_reads.xml
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| Tue, 06 Nov 2012 11:48:49 -0600 |
Jim Johnson |
Fix dir path to GenomeAnalysisTKLite.jar
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| Tue, 06 Nov 2012 11:41:15 -0600 |
Jim Johnson |
Update tool_dependencies.xml
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| Tue, 06 Nov 2012 11:23:22 -0600 |
Jim Johnson |
Cleanup reduce_reads.xml
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| Tue, 06 Nov 2012 10:32:16 -0600 |
Jim Johnson |
ReduceReads added
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| Fri, 02 Nov 2012 13:47:22 -0500 |
Jim Johnson |
Quote the tool_dependencies.xml GATK2_SITE_OPTIONS action text
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| Thu, 01 Nov 2012 14:30:06 -0500 |
Jim Johnson |
tool_dependencies.xml - fix set_environment
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| Thu, 01 Nov 2012 14:19:38 -0500 |
Jim Johnson |
tool_dependencies.xml - fix move_file and add symlink
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| Thu, 01 Nov 2012 14:00:40 -0500 |
Jim Johnson |
tool_dependencies.xml - fix move_file and add symlink
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| Thu, 01 Nov 2012 13:44:41 -0500 |
Jim Johnson |
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
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| Thu, 01 Nov 2012 13:53:22 -0400 |
jjohnson |
Uploaded
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