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43
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1 #!/bin/bash
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2
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3 # Check java version
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4 if (type -p java >> /dev/null); then
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5 _java=java
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6 elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]; then
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7 _java="$JAVA_HOME/bin/java"
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8 else
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9 echo "You must install java before runing this tool"
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10 exit 1
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11 fi
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12 if [[ "$_java" ]]; then
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13 version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
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14 if ! [[ "$version" > "1.6" ]]; then
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15 echo "Java version should be > 1.6"
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16 exit 1
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17 fi
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18 fi
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19
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20 # Locate the jar directory
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21 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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22 jar_path="${DIR}/${1}"
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23 shift
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24
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25 # Untar the chromosome file into a temporary directory
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26 tar_file="$1"
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27 shift
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28 tmp_dir="/tmp/$(basename "$tar_file")"
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29 mkdir -p $tmp_dir
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30 tar -C $tmp_dir -xvf $tar_file
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31
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32 # Run the jar and remove the temporary directory
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33 java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
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34 rm -rf $tmp_dir
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