blob: d105ecad017efcc4bbf0e13a29d010d24b63b39b (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
|
#!/usr/bin/env bash
set -eou pipefail
export LC_ALL=en_US.UTF-8
default_jvm_mem_opts="-Xms512m -Xmx1g"
jvm_mem_opts=""
jvm_prop_opts=""
pass_args=""
for arg in "$@"; do
case $arg in
'-D'*)
jvm_prop_opts="$jvm_prop_opts $arg"
;;
'-XX'*)
jvm_prop_opts="$jvm_prop_opts $arg"
;;
'-Xm'*)
jvm_mem_opts="$jvm_mem_opts $arg"
;;
*)
pass_args="$pass_args $arg"
;;
esac
done
if [ "$jvm_mem_opts" == "" ]; then
jvm_mem_opts="$default_jvm_mem_opts"
fi
pass_arr=($pass_args)
if [[ ${pass_arr[0]:=} == org* ]]
then
eval java $jvm_mem_opts $jvm_prop_opts -cp '/usr/share/java/gatk-bin/GenomeAnalysisTK.jar' $pass_args
else
eval java $jvm_mem_opts $jvm_prop_opts -jar '/usr/share/java/gatk-bin/GenomeAnalysisTK.jar' $pass_args
fi
exit
|