Mercurial > repos > marc-wilkins > samifier
view samifier/result_analyser.sh @ 2:66ad014e6975 draft default tip
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author | marc-wilkins |
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date | Tue, 06 Aug 2013 20:43:24 -0400 |
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#!/bin/bash # Check java version if (type -p java >> /dev/null); then _java=java elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]; then _java="$JAVA_HOME/bin/java" else echo "You must install java before runing this tool" exit 1 fi if [[ "$_java" ]]; then version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}') if ! [[ "$version" > "1.6" ]]; then echo "Java version should be > 1.6" exit 1 fi fi # Locate the jar directory DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" jar_path="${DIR}/${1}" shift # Untar the chromosome file into a temporary directory tar_file="$1" shift tmp_dir="/tmp/$(basename "$tar_file")" mkdir -p $tmp_dir tar -C $tmp_dir -xvf $tar_file # Run the jar and remove the temporary directory java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir" rm -rf $tmp_dir