From 45ce7f4be985fa86e5da14dc903e959d9a9451ae Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Mar 2019 15:24:32 +0100
Subject: [PATCH] update_tools.sh: auto update for singularity docker and nf
modules
---
src/update_tools.sh | 71 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 71 insertions(+)
create mode 100755 src/update_tools.sh
diff --git a/src/update_tools.sh b/src/update_tools.sh
new file mode 100755
index 0000000..9345078
--- /dev/null
+++ b/src/update_tools.sh
@@ -0,0 +1,71 @@
+#/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
--
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