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view galaxy-conf/galaxyToolRunner.sh @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents eb53be9a09f4
children
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#!/usr/bin/env bash

if [ $# -eq 0 ]
then
  echo "USAGE: galaxyToolRunner.sh APPNAME [ARGS]";
  exit;
fi

# Verify that the user has Java 7 installed
# Otherwise there will be an obscure UnsupportedClassVersion error
version=$(java -version 2>&1 | awk -F '"' '/version/ {print $2}')
if [[ "$version" < "1.7" ]]; then
    echo "Need Java 7 or greater. You have Java $version installed."
    exit
fi

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
java -Dlog4j.configuration=log4j.properties -cp $DIR:$DIR/../build:$DIR/../dist/*:$DIR/../lib/* edu.unc.genomics."$@"