Newer
Older
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
#/bin/sh
# A POSIX variable
OPTIND=1
# Initialize our own variables:
tool=""
version=""
while getopts "h?v:t:p:" opt; do
case "$opt" in
h|\?)
echo "update_tools.sh -t toolname -v tool_version -p tool_previous_version"
exit 0
;;
v)
version=$OPTARG
;;
p)
prev_version=$OPTARG
;;
t)
tool=$OPTARG
;;
esac
done
echo "tool=$tool, version='$version'"
docker_tool_dir="src/docker_modules/"$tool"/"
echo $docker_tool_dir
if [ -d $docker_tool_dir ]; then
echo "docker module found for $tool."
if [ -d $docker_tool_dir$version ]; then
echo "version already existing, skipping."
else
cp -R $docker_tool_dir$prev_version $docker_tool_dir$version
sed -i "s|$prev_version|$version|g" "$docker_tool_dir$version/Dockerfile"
sed -i "s|$prev_version|$version|g" "$docker_tool_dir$version/docker_init.sh"
echo "docker_module for $tool:$version, done."
fi
else
echo "docker module not found for '$tool', skipping."
fi
singularity_tool_dir="src/singularity_modules/"$tool"/"
echo $singularity_tool_dir
if [ -d $singularity_tool_dir ]; then
echo "singularity module found for $tool."
if [ -d $singularity_tool_dir$version ]; then
echo "version already existing, skipping."
else
cp -R $singularity_tool_dir$prev_version $singularity_tool_dir$version
sed -i "s|$prev_version|$version|g" "$singularity_tool_dir$version/$tool.def"
sed -i "s|$prev_version|$version|g" "$singularity_tool_dir$version/build.sh"
echo "singularity_module for $tool:$version, done."
fi
else
echo "singularity module not found for '$tool', skipping."
fi
nf_tool_dir="src/nf_modules/"$tool"/"
echo $nf_tool_dir
if [ -d $nf_tool_dir ]; then
echo "nf module found for $tool."
find $nf_tool_dir -maxdepth 1 -mindepth 1 -type f -name "*.config" |
awk "{system(\"sed -i \\\"s|$prev_version|$version|g\\\" \"\$0)}"
echo "nf_module for $tool:$version, done."
else
echo "nf module not found for '$tool', skipping."
fi