Mercurial > repos > marc-wilkins > samifier
comparison samifier/samifier.sh @ 2:66ad014e6975 draft default tip
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| author | marc-wilkins |
|---|---|
| date | Tue, 06 Aug 2013 20:43:24 -0400 |
| parents | |
| children |
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| 1:afa0439120d8 | 2:66ad014e6975 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 # Check java version | |
| 4 if (type -p java >> /dev/null); then | |
| 5 _java=java | |
| 6 elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]; then | |
| 7 _java="$JAVA_HOME/bin/java" | |
| 8 else | |
| 9 echo "You must install java before runing this tool" | |
| 10 exit 1 | |
| 11 fi | |
| 12 if [[ "$_java" ]]; then | |
| 13 version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}') | |
| 14 if ! [[ "$version" > "1.6" ]]; then | |
| 15 echo "Java version should be > 1.6" | |
| 16 exit 1 | |
| 17 fi | |
| 18 fi | |
| 19 | |
| 20 # Locate the jar directory | |
| 21 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" | |
| 22 jar_path="${DIR}/${1}" | |
| 23 shift | |
| 24 | |
| 25 # Untar the chromosome file into a temporary directory | |
| 26 tar_file="$1" | |
| 27 shift | |
| 28 tmp_dir="/tmp/$(basename "$tar_file")" | |
| 29 mkdir -p $tmp_dir | |
| 30 tar -C $tmp_dir -xvf $tar_file | |
| 31 | |
| 32 # Run the jar and remove the temporary directory | |
| 33 java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir" | |
| 34 rm -rf $tmp_dir |