1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fd76a4474535/ changeset: fd76a4474535 user: dan date: 2011-11-21 14:52:13 summary: Add picard_FastqToSam.xml and picard_SamToFastq.xml to tool_conf.xml.main. affected #: 3 files diff -r 830ea4877c7b05d1b58c3771be9adb481639d83b -r fd76a44745351d69f8abbccc14fec833e83b469a tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -406,6 +406,9 @@ <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section><section name="NGS: Picard (beta)" id="picard_beta"> + <label text="Conversion" id="picard_conversion"/> + <tool file="picard/picard_FastqToSam.xml" /> + <tool file="picard/picard_SamToFastq.xml" /><label text="QC/Metrics for sam/bam" id="qcsambam"/><tool file="picard/picard_BamIndexStats.xml" /><tool file="picard/rgPicardASMetrics.xml" /> diff -r 830ea4877c7b05d1b58c3771be9adb481639d83b -r fd76a44745351d69f8abbccc14fec833e83b469a tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -1,6 +1,7 @@ <tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0"><description>creates an unaligned BAM file</description> - <requirements><requirement type="package">picard</requirement></requirements> + <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> + <!-- Dan Blankenberg --><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar" FASTQ="${input_fastq1}" diff -r 830ea4877c7b05d1b58c3771be9adb481639d83b -r fd76a44745351d69f8abbccc14fec833e83b469a tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -1,6 +1,7 @@ <tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0"><description>creates a FASTQ file</description> - <requirements><requirement type="package">picard</requirement></requirements> + <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> + <!-- Dan Blankenberg --><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar" INPUT="${input_sam}" 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.