update_tools.sh: add update tool for psmn module

src/update_tools.sh

@@ -8,64 +8,85 @@ tool=""
 version=""
 
 while getopts "h?v:t:p:" opt; do
-  case "$opt" in
+  case "${opt}" in
   h|\?)
     echo "update_tools.sh -t toolname -v tool_version -p tool_previous_version"
     exit 0
     ;;
   v)
-    version=$OPTARG
+    version=${OPTARG}
     ;;
   p)
-    prev_version=$OPTARG
+    prev_version=${OPTARG}
     ;;
   t)
-    tool=$OPTARG
+    tool=${OPTARG}
     ;;
   esac
 done
 
-echo "tool=$tool, version='$version'"
+echo "tool=${tool}, version='${version}', previous 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
+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."
+    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 '$tool', skipping."
+  echo "docker module not found for '${tool}', skipping."
 fi
 
-singularity_tool_dir="src/singularity_modules/"$tool"/"
-echo $singularity_tool_dir
-if [ -d $singularity_tool_dir ]; then
+singularity_tool_dir="src/singularity_modules/"${tool}"/"
+echo ${singularity_tool_dir}
+if [ -d ${singularity_tool_dir} ]; then
   echo "singularity module found for $tool."
-  if [ -d $singularity_tool_dir$version ]; then
+  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."
+    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 '$tool', skipping."
+  echo "singularity module not found for '${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."
+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 '$tool', skipping."
+  echo "nf module not found for '${tool}', skipping."
+fi
+
+psmn_modules_dir="src/psmn_modules/.git/"
+if [ ! -d ${nf_tool_dir} ]; then
+  git submodule init && \
+  git submodule update
+fi
+psmn_tool_app_dir="src/psmn_modules/apps/"${tool}"/"
+psmn_tool_module_dir="src/psmn_modules/modulefiles/"${tool}"/"
+echo ${psmn_tool_app_dir}
+if [ -d ${psmn_tool_app_dir} ]; then
+  echo "psmn module found for ${tool}."
+  cp ${psmn_tool_app_dir}/install_${prev_version}.sh \
+    ${psmn_tool_app_dir}/install_${version}.sh
+  sed -i "s|$prev_version|$version|g" ${psmn_tool_app_dir}/install_${version}.sh
+  cp ${psmn_tool_module_dir}/${prev_version}.lua \
+    ${psmn_tool_module_dir}/${version}.lua
+  sed -i "s|${prev_version}|${version}|g" ${psmn_tool_module_dir}/${version}.lua
+  echo "psmn_module for ${tool}:${version}, done."
+else
+  echo "psmn module not found for '${tool}', skipping."
 fi