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mjhsieh/gist:3d35fde8686ca4631ab3

Created December 8, 2014 17:22
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gistfile1.sh-session
$ cat analysis/bin/saxonb9 analysis/bin/smrtreporter analysis/bin/referenceUploader
#!/bin/bash
# Source the smrtanalysis setup.sh file
. $($(dirname $(readlink -f "$0"))/../../admin/bin/getsetupfile)
JAVA=${SMRT_TOPDIR}/redist/java/bin/java
JAVA_OPTIONS="-Xmx72m -Xms4m"
$JAVA $JAVA_OPTIONS -jar $ASSEMBLY_HOME/lib/saxonb9-1-0-1j/saxon9.jar "$@"
#!/bin/bash
# Source the smrtanalysis setup.sh file
. $($(dirname $(readlink -f "$0"))/../../admin/bin/getsetupfile)
JAVA_OPTIONS="-Xmx72m -Xms4m"
java $JAVA_OPTIONS -jar ${SMRT_TOPDIR}/analysis/lib/java/secondary-analysis-smrtreporter-2.3.0-SNAPSHOT.jar "$@"
#!/bin/bash
# Source the smrtanalysis setup.sh file
. $($(dirname $(readlink -f "$0"))/../../admin/bin/getsetupfile)
JAVA_OPTIONS="-Xmx512m -Xms4m"
java $JAVA_OPTIONS -jar ${SMRT_TOPDIR}/analysis/lib/java/secondary-analysis-referenceUploader-2.3.0-SNAPSHOT.jar "$@"
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