je_markdupes: je annotate

annotate je @ 3:4ccf1406832d draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty

author	gbcs-embl-heidelberg
date	Wed, 21 Jun 2017 05:23:33 -0400
parents	c6afeeade4f2
children	384b972e43bc

rev	line source
0 d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	1 #!/bin/sh
3 4ccf1406832d planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty gbcs-embl-heidelberg parents: 1 diff changeset	2 # Wrapper around je_1.1_bundle.jar
0 d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	3
d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	4 # where are we stored ?
d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	5 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	6 # echo $DIR
d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	7 # path to jar file to execute, this jar is supposed to be in the same dir as this script
3 4ccf1406832d planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty gbcs-embl-heidelberg parents: 1 diff changeset	8 JAR_FILE=$DIR"/je_1.1_bundle.jar"
0 d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	9
1 c6afeeade4f2 use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	10 # set default _JAVA_OPTIONS
c6afeeade4f2 use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	11 _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}
c6afeeade4f2 use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	12 export _JAVA_OPTIONS
c6afeeade4f2 use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	13
c6afeeade4f2 use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	14 # uncomment to change logging level using your own log4j.xml found in $DIR file
c6afeeade4f2 use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	15 # OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml"
0 d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	16
d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	17 java $OPTS -jar $JAR_FILE "$@"
d39a96961423 Initial upload gbcs-embl-heidelberg parents: diff changeset	18 exit $?