commit/galaxy-central: 2 new changesets
2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8cb402826d49/ changeset: 8cb402826d49 user: fubar date: 2011-08-04 08:50:22 summary: sam_merge.xml tweaks: changed call to MergeSamFiles to use minimal command line flags and finally got LENIENT validation stringency to actually work affected #: 3 files (9 bytes) --- a/test-data/sam_merge_out1.log Thu Aug 04 12:43:30 2011 +1000 +++ b/test-data/sam_merge_out1.log Thu Aug 04 16:50:22 2011 +1000 @@ -1,5 +1,5 @@ -[Thu Aug 04 12:17:33 EST 2011] net.sf.picard.sam.MergeSamFiles INPUT=[/data/tmp/tmp6eiFcc/database/files/000/dataset_1.dat, /data/tmp/tmp6eiFcc/database/files/000/dataset_2.dat, /data/tmp/tmp6eiFcc/database/files/000/dataset_2.dat] OUTPUT=/data/tmp/tmp6eiFcc/database/files/000/dataset_3.dat MERGE_SEQUENCE_DICTIONARIES=true SORT_ORDER=coordinate ASSUME_SORTED=false USE_THREADING=false TMP_DIR=/tmp/rlazarus VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -INFO 2011-08-04 12:17:33 MergeSamFiles Sorting input files using temp directory /tmp/rlazarus -INFO 2011-08-04 12:17:33 MergeSamFiles Finished reading inputs. -[Thu Aug 04 12:17:33 EST 2011] net.sf.picard.sam.MergeSamFiles done. +[Thu Aug 04 13:48:49 EST 2011] net.sf.picard.sam.MergeSamFiles INPUT=[/data/tmp/tmpjnE9mC/database/files/000/dataset_1.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_2.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_2.dat] OUTPUT=/data/tmp/tmpjnE9mC/database/files/000/dataset_3.dat MERGE_SEQUENCE_DICTIONARIES=true VALIDATION_STRINGENCY=LENIENT SORT_ORDER=coordinate ASSUME_SORTED=false USE_THREADING=false TMP_DIR=/tmp/rlazarus VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +INFO 2011-08-04 13:48:49 MergeSamFiles Sorting input files using temp directory /tmp/rlazarus +INFO 2011-08-04 13:48:49 MergeSamFiles Finished reading inputs. +[Thu Aug 04 13:48:49 EST 2011] net.sf.picard.sam.MergeSamFiles done. Runtime.totalMemory()=2028732416 --- a/test-data/sam_merge_out2.log Thu Aug 04 12:43:30 2011 +1000 +++ b/test-data/sam_merge_out2.log Thu Aug 04 16:50:22 2011 +1000 @@ -1,5 +1,5 @@ -[Thu Aug 04 12:18:15 EST 2011] net.sf.picard.sam.MergeSamFiles INPUT=[/data/tmp/tmp6eiFcc/database/files/000/dataset_5.dat, /data/tmp/tmp6eiFcc/database/files/000/dataset_6.dat, /data/tmp/tmp6eiFcc/database/files/000/dataset_7.dat] OUTPUT=/data/tmp/tmp6eiFcc/database/files/000/dataset_8.dat MERGE_SEQUENCE_DICTIONARIES=true SORT_ORDER=coordinate ASSUME_SORTED=false USE_THREADING=false TMP_DIR=/tmp/rlazarus VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -INFO 2011-08-04 12:18:15 MergeSamFiles Sorting input files using temp directory /tmp/rlazarus -INFO 2011-08-04 12:18:15 MergeSamFiles Finished reading inputs. -[Thu Aug 04 12:18:15 EST 2011] net.sf.picard.sam.MergeSamFiles done. +[Thu Aug 04 13:49:53 EST 2011] net.sf.picard.sam.MergeSamFiles INPUT=[/data/tmp/tmpjnE9mC/database/files/000/dataset_5.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_6.dat, /data/tmp/tmpjnE9mC/database/files/000/dataset_7.dat] OUTPUT=/data/tmp/tmpjnE9mC/database/files/000/dataset_8.dat MERGE_SEQUENCE_DICTIONARIES=true VALIDATION_STRINGENCY=LENIENT SORT_ORDER=coordinate ASSUME_SORTED=false USE_THREADING=false TMP_DIR=/tmp/rlazarus VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +INFO 2011-08-04 13:49:54 MergeSamFiles Sorting input files using temp directory /tmp/rlazarus +INFO 2011-08-04 13:49:54 MergeSamFiles Finished reading inputs. +[Thu Aug 04 13:49:54 EST 2011] net.sf.picard.sam.MergeSamFiles done. Runtime.totalMemory()=2028732416 --- a/tools/samtools/sam_merge.xml Thu Aug 04 12:43:30 2011 +1000 +++ b/tools/samtools/sam_merge.xml Thu Aug 04 16:50:22 2011 +1000 @@ -4,9 +4,9 @@ <requirement type="package">picard</requirement></requirements><command> - java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MERGE_SEQUENCE_DICTIONARIES=$mergeSD OUTPUT=$output1 INPUT=$input1 INPUT=$input2 +java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 #for $i in $inputs - INPUT=${i.input} + I=${i.input} #end for 2> $outlog </command> http://bitbucket.org/galaxy/galaxy-central/changeset/95e1527499e0/ changeset: 95e1527499e0 user: fubar date: 2011-08-04 08:55:13 summary: Increase lines_diff so sam_merge tests might pass on buildbot affected #: 1 file (2 bytes) --- a/tools/samtools/sam_merge.xml Thu Aug 04 16:50:22 2011 +1000 +++ b/tools/samtools/sam_merge.xml Thu Aug 04 16:55:13 2011 +1000 @@ -36,7 +36,7 @@ <param name="input1" value="sam_merge_in1.bam" ftype="bam" /><param name="input2" value="sam_merge_in2.bam" ftype="bam" /><output name="output1" file="sam_merge_out1.bam" ftype="bam" /> - <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="8"/> + <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="10"/></test><test><param name="title" value="test2" /> @@ -45,7 +45,7 @@ <param name="input2" value="sam_merge_in2.bam" ftype="bam" /><param name="input" value="sam_merge_in3.bam" ftype="bam" /><output name="output1" file="sam_merge_out2.bam" ftype="bam" /> - <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="8"/> + <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="10"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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