forked from galaxyproject/pulsar
-
Notifications
You must be signed in to change notification settings - Fork 0
/
update_galaxy_utils.sh
executable file
·86 lines (67 loc) · 2.63 KB
/
update_galaxy_utils.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
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
#!/bin/bash
usage() {
cat << EOF
Usage: ${0##*/} [-i] /path/to/galaxy...
Sync Pulsar shared modules to those same modules in Galaxy directory (or vice versa if -i).
EOF
}
if [ $# -lt 1 ]; then
usage
exit 1
fi
invert=0
OPTIND=1
while getopts ":i" opt; do
case "$opt" in
h)
usage
exit 0
;;
i)
invert=1
;;
'?')
usage >&2
exit 1
;;
esac
done
shift "$((OPTIND-1))" # Shift off the options and optional --.
PULSAR_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
GALAXY_DIRECTORY=$1
GALAXY_LIB_DIR=$GALAXY_DIRECTORY/lib/galaxy
GALAXY_RUNNERS_DIRECTORY=$GALAXY_LIB_DIR/jobs/runners
if [ "$invert" -ne "1" ];
then
rm -rf $GALAXY_RUNNERS_DIRECTORY/util
cp -r $PULSAR_DIRECTORY/pulsar/managers/util $GALAXY_RUNNERS_DIRECTORY
rm -rf $GALAXY_LIB_DIR/objectstore
cp -r $PULSAR_DIRECTORY/galaxy/objectstore $GALAXY_LIB_DIR
rm -rf $GALAXY_LIB_DIR/tools/deps
cp -r $PULSAR_DIRECTORY/galaxy/tools/deps $GALAXY_LIB_DIR/tools
rm -rf $GALAXY_LIB_DIR/jobs/metrics
cp -r $PULSAR_DIRECTORY/galaxy/jobs/metrics $GALAXY_LIB_DIR/jobs
rm -rf $GALAXY_LIB_DIR/tools/linters
cp -r $PULSAR_DIRECTORY/galaxy/tools/linters $GALAXY_LIB_DIR/tools
cp $PULSAR_DIRECTORY/galaxy/tools/lint.py $GALAXY_LIB_DIR/tools/lint.py
cp $PULSAR_DIRECTORY/galaxy/tools/loader.py $GALAXY_LIB_DIR/tools/loader.py
cp $PULSAR_DIRECTORY/galaxy/tools/loader_directory.py $GALAXY_LIB_DIR/tools/loader_directory.py
cp $PULSAR_DIRECTORY/galaxy/util/plugin_config.py $GALAXY_LIB_DIR/util
cp $PULSAR_DIRECTORY/galaxy/util/xml_macros.py $GALAXY_LIB_DIR/util
else
rm -rf $PULSAR_DIRECTORY/pulsar/managers/util
cp -r $GALAXY_RUNNERS_DIRECTORY/util $PULSAR_DIRECTORY/pulsar/managers
rm -rf $PULSAR_DIRECTORY/galaxy/objectstore
cp -r $GALAXY_LIB_DIR/objectstore $PULSAR_DIRECTORY/galaxy
rm -rf $PULSAR_DIRECTORY/galaxy/tools/deps
cp -r $GALAXY_LIB_DIR/tools/deps $PULSAR_DIRECTORY/galaxy/tools
rm -rf $PULSAR_DIRECTORY/galaxy/jobs/metrics
cp -r $GALAXY_LIB_DIR/jobs/metrics $PULSAR_DIRECTORY/galaxy/jobs
rm -rf $PULSAR_DIRECTORY/galaxy/tools/linters
cp -r $GALAXY_LIB_DIR/tools/linters $PULSAR_DIRECTORY/galaxy/tools
cp $GALAXY_LIB_DIR/tools/lint.py $PULSAR_DIRECTORY/galaxy/tools
cp $GALAXY_LIB_DIR/tools/loader.py $PULSAR_DIRECTORY/galaxy/tools
cp $GALAXY_LIB_DIR/tools/loader_directory.py $PULSAR_DIRECTORY/galaxy/tools
cp $GALAXY_LIB_DIR/util/plugin_config.py $PULSAR_DIRECTORY/galaxy/util/
cp $GALAXY_LIB_DIR/util/xml_macros.py $PULSAR_DIRECTORY/galaxy/util/
fi