je_demultiplex_illu: je annotate

annotate je @ 4:7895e352c09b draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 1c7680ac36888721d2c0b72f4e6d27415fe07b43

author	gbcs-embl-heidelberg
date	Tue, 01 Aug 2017 03:42:23 -0400
parents	01fdc6d10660
children

rev	line source
0 111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	1 #!/bin/sh
3 01fdc6d10660 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 111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	3
111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	4 # where are we stored ?
111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	5 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	6 # echo $DIR
111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	7 # path to jar file to execute, this jar is supposed to be in the same dir as this script
4 7895e352c09b planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 1c7680ac36888721d2c0b72f4e6d27415fe07b43 gbcs-embl-heidelberg parents: 3 diff changeset	8 JAR_FILE=$DIR"/je_1.2_bundle.jar"
0 111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	9
1 ff5fddc4739b use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	10 # set default _JAVA_OPTIONS
ff5fddc4739b use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	11 _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}
ff5fddc4739b use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	12 export _JAVA_OPTIONS
ff5fddc4739b use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	13
ff5fddc4739b 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 $DIR file
ff5fddc4739b use _JAVA_OPTIONS to set default memory limit gbcs-embl-heidelberg parents: 0 diff changeset	15 # OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml"
0 111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	16
111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	17 java $OPTS -jar $JAR_FILE "$@"
111ba1180318 Initial upload gbcs-embl-heidelberg parents: diff changeset	18 exit $?