Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/galaxyToolRunner.sh @ 12:81d5b81fb3c2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents 4b32ed5d4a1b
children eb53be9a09f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
1 #!/usr/bin/env bash
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
2
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
3 if [ $# -eq 0 ]
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 then
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
5 echo "USAGE: galaxyToolRunner.sh APPNAME [ARGS]";
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
6 exit;
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
7 fi
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 if [ "$1" = "list" ]
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10 then
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
11 find src/edu/unc/genomics/**/*.java -exec basename -s .java {} \;
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
12 fi
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
13
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
14 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
15 java -Dlog4j.configuration=log4j.properties -cp $DIR:$DIR/../build:$DIR/../dist/*:$DIR/../lib/* edu.unc.genomics."$@"