forked from virtualcell/vcell
/
docker_run.sh
executable file
·33 lines (30 loc) · 1.04 KB
/
docker_run.sh
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
#!/bin/bash
show_help() {
echo "usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v]"
echo " OPTIONS and ARGUMENTS:"
echo " -h,--help show this help message and exit"
echo ""
echo " -i,--archive <arg> Path to OMEX/COMBINE Archive file which contains one or more SED-ML encoded simulation experiments"
echo ""
echo " -o,--out-dir <arg> Directory to save outputs"
echo ""
echo " -q,--quiet Suppress all console output"
echo ""
echo " -v,--version Shows program's version number and exit"
echo ""
exit 1
}
if [[ $# -lt 1 ]]; then
show_help
fi
java \
-classpath '/usr/local/app/vcell/lib/*' \
-Dvcell.installDir=/usr/local/app/vcell/installDir \
-Dvcell.server.id="7.3.0.16" \
-Dvcell.cli="true" \
-Dvcell.python.executable=/usr/bin/python3 \
-Dvcell.mongodb.database="localhost" \
-Dvcell.mongodb.host.internal="localhost" \
-Dvcell.mongodb.port.internal=27017 \
-Dcli.workingDir=/usr/local/app/vcell/installDir/python/vcell_cli_utils/ \
org.vcell.cli.CLIStandalone "$@"