|
2
|
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
|
