Merge pull request #93 from CCBR/install-script

Create install script for pipeline usage within ccbrpipeliner

carlisle

@@ -14,7 +14,6 @@ SNAKEMAKE_VERSION="snakemake/7.19.1"
 SINGULARITY_VERSION="singularity/3.10.5"
 
 set -eo pipefail
-module purge
 
 SCRIPTNAME="$0"
 SCRIPTBASENAME=$(readlink -f $(basename $0))
@@ -28,29 +27,27 @@ tools_specific_yaml="tools_biowulf.yaml"
 # essential files
 # these are relative to the workflows' base folder
 # these are copied into the WORKDIR
-ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml resources/cluster_* resources/tools_*"
-ESSENTIAL_FOLDERS="workflow/scripts"
+ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml"
+ESSENTIAL_FOLDERS="workflow/scripts annotation"
 # set extra singularity bindings
 EXTRA_SINGULARITY_BINDS="-B /data/CCBR_Pipeliner/,/lscratch"
 
-function get_git_commitid_tag() {
-  # This function gets the latest git commit id and tag
-  # Input is PIPELINE_HOME folder which is a git folder
-    cd $1
-    gid=$(git rev-parse HEAD)
-    tag=$(git describe --tags $gid 2>/dev/null)
-    echo -ne "$gid\t$tag"
-}
-
 # ## setting PIPELINE_HOME
 PIPELINE_HOME=$(readlink -f $(dirname "$0"))
 echo "Pipeline Dir: $PIPELINE_HOME"
 # set snakefile
 SNAKEFILE="${PIPELINE_HOME}/workflow/Snakefile"
 
-# get github commit tag
-GIT_COMMIT_TAG=$(get_git_commitid_tag $PIPELINE_HOME)
-echo "Git Commit/Tag: $GIT_COMMIT_TAG"
+function get_version_from_path() {
+  PIPELINE_HOME=$1
+  VERSION="$(echo $PIPELINE_HOME | grep -oP 'v(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?' - )"
+  echo -ne $VERSION
+}
+
+# get version from directory name
+# regex source: https://semver.org/#is-there-a-suggested-regular-expression-regex-to-check-a-semver-string
+#echo "Version: $VERSION"
+echo "Version: $(get_version_from_path $PIPELINE_HOME)"
 
 function usage() { 
 # This function prints generic usage of the wrapper script.
@@ -104,8 +101,8 @@ function init() {
   done
 
   # rename config dependent on partition used
-  cp $WORKDIR/config/$cluster_specific_yaml $WORKDIR/config/cluster.yaml
-  cp $WORKDIR/config/$tools_specific_yaml $WORKDIR/config/tools.yaml
+  cp ${PIPELINE_HOME}/resources/$cluster_specific_yaml $WORKDIR/config/cluster.yaml
+  cp ${PIPELINE_HOME}/resources/$tools_specific_yaml $WORKDIR/config/tools.yaml
 
   # copy essential folders
   for f in $ESSENTIAL_FOLDERS;do
@@ -443,4 +440,4 @@ function main(){
 }
 
 # call the main function
-main "$@"
+main "$@"

install.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+# usage:
+#   ./install.sh new/path/to/install
+# examples
+#   ./install.sh .v2.4.0
+#   /data/CCBR_Pipeliner/Pipelines/CARLISLE/dev/install.sh /data/CCBR_Pipeliner/Pipelines/CARLISLE/.v2.5.0-a
+set -euo pipefail
+
+VERSION=$1
+mkdir -p ${VERSION}/bin
+INSTALL_PATH=$(readlink -f ${VERSION}/bin)
+DIRNAME=$(readlink -f $(dirname $0))
+
+if [ -n "$(ls -A $INSTALL_PATH 2>/dev/null)" ]
+then
+    echo "ERROR: directory not empty: ${INSTALL_PATH}"
+    echo $(ls $INSTALL_PATH)
+    exit 1
+fi
+
+# copy essential files & directories
+
+## carlisle CLI script
+cp $DIRNAME/carlisle $INSTALL_PATH/
+
+## all config & workflow scripts;
+for subdir in annotation config workflow resources .test
+do  
+    mkdir -p ${INSTALL_PATH}/$subdir
+    cp -r ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir
+done
+
+# export path
+if [[ ":$PATH:" != *":${INSTALL_PATH}:"* ]];then
+    export PATH="${PATH}:${INSTALL_PATH}"
+fi
+
+echo "${INSTALL_PATH}"