1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/99419b4be32d/ changeset: 99419b4be32d user: fubar date: 2012-04-03 23:56:46 summary: Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space. affected #: 5 files diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_BamIndexStats.xml --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -7,6 +7,7 @@ -t "$htmlfile" -d "$htmlfile.files_path" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/BamIndexStats.jar" + --tmpdir "${__new_file_path__}" </command><inputs><param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -4,6 +4,7 @@ <!-- Dan Blankenberg --><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar" + --tmpdir "${__new_file_path__}" FASTQ="${input_fastq1}" #if str( $input_fastq2) != "None": FASTQ2="${input_fastq2}" diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_MarkDuplicates.xml --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -7,6 +7,7 @@ --opt-dup-dist="$optDupeDist" --output-format=$outputFormat --output-txt=$outMetrics + --tmpdir "${__new_file_path__}" #if str( $outputFormat ) == "sam" #if str( $remDups ) == "true" --output-sam=$outFileSamRemoved diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -15,6 +15,7 @@ --allow-contig-len-discord=$allowContigLenDiscord --output-format=$outputFormat --output=$outFile + --tmpdir "${__new_file_path__}" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReorderSam.jar" </command><inputs> diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -2,7 +2,7 @@ <command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar + -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}" #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else 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.