4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ccbeeccc70b/ Changeset: 6ccbeeccc70b Branch: srma_memory User: lance_parsons Date: 2014-09-04 20:12:51+00:00 Summary: SRMA tool requires at least 2048m memory and LENIENT validation stringency Affected #: 1 file diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 6ccbeeccc70bc8e2e489f621d13a64f494ae2518 tools/sr_mapping/srma_wrapper.py --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -142,6 +142,8 @@ else: range = options.range srma_cmds = "OFFSET=%s MIN_MAPQ=%s MINIMUM_ALLELE_PROBABILITY=%s MINIMUM_ALLELE_COVERAGE=%s RANGES=%s RANGE=%s CORRECT_BASES=%s USE_SEQUENCE_QUALITIES=%s MAX_HEAP_SIZE=%s" % ( options.offset, options.minMappingQuality, options.minAlleleProbability, options.minAlleleCoverage, ranges, range, options.correctBases, options.useSequenceQualities, options.maxHeapSize ) + + srma_cmds = "%s VALIDATION_STRINGENCY=LENIENT" % srma_cmds # perform alignments buffsize = 1048576 @@ -155,7 +157,7 @@ #create a temp output name, ending in .bam due to required naming conventions? unkown if required output_bam_filename = os.path.join( tmp_dir, "%s.bam" % os.path.split( options.output )[-1] ) # generate commandline - cmd = 'java -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds ) + cmd = 'java -Xmx2048m -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds ) # need to nest try-except in try-finally to handle 2.4 try: https://bitbucket.org/galaxy/galaxy-central/commits/bb4faa5a3b19/ Changeset: bb4faa5a3b19 User: jmchilton Date: 2014-09-22 17:17:11+00:00 Summary: Merge pull request #489. Thanks Lance! Affected #: 1 file diff -r 579d211c2b0fa8ef4195930cb999edbb9a0cf8eb -r bb4faa5a3b1957b2ea220a94ee2315e22354a3cf tools/sr_mapping/srma_wrapper.py --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -142,6 +142,8 @@ else: range = options.range srma_cmds = "OFFSET=%s MIN_MAPQ=%s MINIMUM_ALLELE_PROBABILITY=%s MINIMUM_ALLELE_COVERAGE=%s RANGES=%s RANGE=%s CORRECT_BASES=%s USE_SEQUENCE_QUALITIES=%s MAX_HEAP_SIZE=%s" % ( options.offset, options.minMappingQuality, options.minAlleleProbability, options.minAlleleCoverage, ranges, range, options.correctBases, options.useSequenceQualities, options.maxHeapSize ) + + srma_cmds = "%s VALIDATION_STRINGENCY=LENIENT" % srma_cmds # perform alignments buffsize = 1048576 @@ -155,7 +157,7 @@ #create a temp output name, ending in .bam due to required naming conventions? unkown if required output_bam_filename = os.path.join( tmp_dir, "%s.bam" % os.path.split( options.output )[-1] ) # generate commandline - cmd = 'java -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds ) + cmd = 'java -Xmx2048m -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds ) # need to nest try-except in try-finally to handle 2.4 try: https://bitbucket.org/galaxy/galaxy-central/commits/35f770b6bed8/ Changeset: 35f770b6bed8 Branch: srma_memory User: jmchilton Date: 2014-09-22 17:18:07+00:00 Summary: Close branch. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/f9e429b15b0e/ Changeset: f9e429b15b0e User: jmchilton Date: 2014-09-22 17:20:49+00:00 Summary: Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS. As discussed here https://bitbucket.org/galaxy/galaxy-central/pull-request/489/srma-tool-requi.... Thanks to Bjoern for input. Affected #: 1 file diff -r bb4faa5a3b1957b2ea220a94ee2315e22354a3cf -r f9e429b15b0eacada3a248d14e9b9dcc9be67ed5 tools/sr_mapping/srma_wrapper.py --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -157,8 +157,10 @@ #create a temp output name, ending in .bam due to required naming conventions? unkown if required output_bam_filename = os.path.join( tmp_dir, "%s.bam" % os.path.split( options.output )[-1] ) # generate commandline - cmd = 'java -Xmx2048m -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds ) - + java_opts = '' + if '_JAVA_OPTIONS' not in os.environ: + java_opts = '-Xmx2048m' + cmd = 'java %s -jar %s I=%s O=%s R=%s %s' % ( java_opts, os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds ) # need to nest try-except in try-finally to handle 2.4 try: try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.