1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/f335b8bbb91f/ changeset: f335b8bbb91f user: dan date: 2011-10-26 19:35:17 summary: "Merge BAM Files" under SAM Tools section(???) calls Picard MergeSamFiles.jar. Update to new jar location. affected #: 1 file

diff -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d -r f335b8bbb91f575f1ffac466c53b907e8623a9a8 tools/samtools/sam_merge.xml --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -4,7 +4,7 @@ <requirement type="package">picard</requirement></requirements><command> -java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 +java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 #for $i in $inputs I=${i.input} #end for @@ -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="10"/> + <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/></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="10"/> + <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/></test></tests><help>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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