src/training_dataset.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 /*
 small pipeline to build a training dataset from whole genome data
 

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}', 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
-    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
-
-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