Ross Lazarus 8a9c206a5b Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py

2012-04-05 02:16:12 +10:00

..

picard_AddOrReplaceReadGroups.xml

Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir "${__new_file_path__}" to the command line generated. That will over-ride the default value "/tmp" for opts.tmpdir in picard_wrapper.py and solve the problem with /tmp filling reported by Matt Shirley.

2012-04-04 06:11:54 +10:00

picard_BamIndexStats.xml

Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.

2012-04-04 07:56:46 +10:00

picard_FastqToSam.xml

Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py

2012-04-05 02:16:12 +10:00

picard_MarkDuplicates.xml

Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.

2012-04-04 07:56:46 +10:00

picard_ReorderSam.xml

Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.

2012-04-04 07:56:46 +10:00

picard_ReplaceSamHeader.xml

Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

2011-11-12 04:25:19 +11:00

picard_SamToFastq_wrapper.py

Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq.

2012-01-25 12:11:27 -05:00

picard_SamToFastq.xml

Enhance Picard SamToFastq to allow read group aware processing.

2012-01-24 15:03:35 -05:00

picard_wrapper.py

Merged in jmchilton/umn-galaxy-central (pull request #28)

2012-01-23 14:44:50 -05:00

rgPicardASMetrics.xml

Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.

2012-04-04 07:56:46 +10:00

rgPicardFixMate.xml

Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

2011-11-12 04:25:19 +11:00

rgPicardGCBiasMetrics.xml

Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table.

2011-11-22 11:56:53 -05:00

rgPicardHsMetrics.xml

Fixed composite download zip file failure related to trying to delete a file whose file handle was needed as the return value

2012-01-19 12:01:20 +11:00

rgPicardInsertSize.xml

Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

2011-11-12 04:25:19 +11:00

rgPicardLibComplexity.xml

Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

2011-11-12 04:25:19 +11:00

rgPicardMarkDups.xml

Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

2011-11-12 04:25:19 +11:00