annotate galaxy-conf/galaxyToolRunner.sh @ 16:35031c567ece
draft
Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
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timpalpant |
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Sat, 09 Jun 2012 16:06:25 -0400 |
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eb53be9a09f4 |
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4
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1 #!/usr/bin/env bash
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2
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3 if [ $# -eq 0 ]
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4 then
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5 echo "USAGE: galaxyToolRunner.sh APPNAME [ARGS]";
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6 exit;
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7 fi
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8
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13
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9 # Verify that the user has Java 7 installed
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10 # Otherwise there will be an obscure UnsupportedClassVersion error
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11 version=$(java -version 2>&1 | awk -F '"' '/version/ {print $2}')
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12 if [[ "$version" < "1.7" ]]; then
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13 echo "Need Java 7 or greater. You have Java $version installed."
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14 exit
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4
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15 fi
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16
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17 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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18 java -Dlog4j.configuration=log4j.properties -cp $DIR:$DIR/../build:$DIR/../dist/*:$DIR/../lib/* edu.unc.genomics."$@" |
