update_tools.sh: auto update for singularity docker and nf modules

src/update_tools.sh

+#/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