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#!/usr/bin/env bash
set -eo pipefail
module purge
# Author: NameHere, PhD
# CCBR, NCI
# (c) 2023
#
# wrapper script to run the snakemake pipeline
# a) on an interactive node (runlocal) OR
# b) submit to the slurm load scheduler (run)
#
# setting python and snakemake versions
PYTHON_VERSION="python/3.9"
SNAKEMAKE_VERSION="snakemake/7.19.1"
#define cluster, partitions dependent on host
hostID=`echo $HOSTNAME`
if [[ $hostID == "biowulf.nih.gov" ]]; then
BUYINPARTITIONS=$(bash <(curl -s https://github.com/raw/CCBR/Tools/master/Biowulf/get_buyin_partition_list.bash 2>/dev/null))
PARTITIONS="norm,ccr"
cluster_specific_yaml="cluster_biowulf.yaml"
tools_specific_yaml="tools_biowulf.yaml"
#if [ $BUYINPARTITIONS ];then PARTITIONS="norm,$BUYINPARTITIONS";fi
elif [[ $hostID == "biowulf8.nih.gov" ]]; then
PARTITIONS="rhel8"
cluster_specific_yaml="cluster_rhel8.yaml"
tools_specific_yaml="tools_rhel8.yaml"
fi
# set extra singularity bindings
EXTRA_SINGULARITY_BINDS="/lscratch, /data/CCBR_Pipeliner/"
SCRIPTNAME="$0"
SCRIPTDIRNAME=$(readlink -f $(dirname $0))
SCRIPTBASENAME=$(readlink -f $(basename $0))
# 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/fqscreen_config.conf config/multiqc_config.yaml resources/cluster_* resources/tools_*"
ESSENTIAL_FOLDERS="workflow/scripts"
function get_git_commitid_tag() {
# This function gets the latest git commit id and tag
# @Input:
# @param1: PIPELINE_HOME folder which is a initialized git repo folder path
# @Output:
# @param1: tab-delimited commit id and tag
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"
echo "Snakefile: $SNAKEFILE"
# get github commit tag
GIT_COMMIT_TAG=$(get_git_commitid_tag $PIPELINE_HOME)
echo "Git Commit/Tag: $GIT_COMMIT_TAG"
function usage() {
# This function prints generic usage of the wrapper script.
echo "${SCRIPTBASENAME}
--> run CARLISLE
Cut And Run anaLysIS pipeLinE
USAGE:
bash ${SCRIPTNAME} -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
Required Arguments:
1. RUNMODE: [Type: String] Valid options:
*) init : initialize workdir
*) run : run with slurm
*) reset : DELETE workdir dir and re-init it
*) dryrun : dry run snakemake to generate DAG
*) unlock : unlock workdir if locked by snakemake
*) runlocal : run without submitting to sbatch
*) testrun: run on cluster with included test dataset
2. WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.
"
}
function err() {
# This is a generic error message function. It prints the message, then the
# usage and exits with non-zero exit code.
# @Input:
# @param1: Message to print before printing the usage and exiting
# @Ouput:
# @param2: echo the error message with the usage to the screen
cat <<< "
#################################################################
##### ERROR ############ ERROR ########## ERROR #################
#################################################################
$@
" && usage_only && exit 1 1>&2;
}
function init() {
# This function initializes the workdir by:
# 1. creating the working dir
# 2. copying essential files like config.yaml and samples.tsv into the workdir
# 3. setting up logs and stats folders
# create output folder
if [ -d $WORKDIR ];then err "Folder $WORKDIR already exists!"; fi
mkdir -p $WORKDIR
# copy essential files
if [[ ! -d $WORKDIR/config ]]; then mkdir $WORKDIR/config; fi
for f in $ESSENTIAL_FILES; do
echo "Copying essential file: $f"
fbn=$(basename $f)
sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/$f > $WORKDIR/config/$fbn
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
# copy essential folders
for f in $ESSENTIAL_FOLDERS;do
rsync -avz --no-perms --no-owner --no-group --progress $PIPELINE_HOME/$f $WORKDIR/
done
#create log and stats folders
if [ ! -d $WORKDIR/logs ]; then mkdir -p $WORKDIR/logs;echo "Logs Dir: $WORKDIR/logs";fi
if [ ! -d $WORKDIR/stats ];then mkdir -p $WORKDIR/stats;echo "Stats Dir: $WORKDIR/stats";fi
echo"#################################################################"
echo"#################################################################"
echo"Done Initializing $WORKDIR."
echo"You can now edit $WORKDIR/config.yaml and $WORKDIR/samples.tsv"
echo"#################################################################"
echo"#################################################################"
}
function check_essential_files() {
# Checks if files essential to start running the pipeline exist in the workdir
# By default config.yaml and samples.tsv are considered essential files.
if [ ! -d $WORKDIR ];then err "Folder $WORKDIR does not exist!"; fi
for f in $ESSENTIAL_FILES; do
fbn=$(basename $f)
if [ ! -f $WORKDIR/config/$fbn ]; then err "Error: '${fbn}' file not found in $WORKDIR ... initialize first!";fi
done
for f in $ESSENTIAL_FOLDERS;do
fbn=$(basename $f)
if [ ! -d $WORKDIR/$fbn ]; then err "Error: '${fbn}' folder not found in $WORKDIR ... initialize first!";fi
done
}
function reconfig(){
# Rebuild config file and replace the config.yaml in the WORKDIR
# this is only for dev purposes when new key-value pairs are being
# updated in the config file in PIPELINE_HOME
check_essential_files
_set_config
echo "$WORKDIR/config.yaml has been updated!"
}
function runcheck(){
# Check "job-essential" files and load required modules
check_essential_files
module load $PYTHON_VERSION
module load $SNAKEMAKE_VERSION
}
function controlcheck(){
# check controls are not listed in comparisons
control_list=`awk '$3 ~ /Y/' ${WORKDIR}/config/samples.tsv | awk '{print $1}'`
check1=`awk '{print $1}' ${WORKDIR}/config/contrasts.tsv`
check2=`awk '{print $2}' ${WORKDIR}/config/contrasts.tsv`
for sample_id in ${control_list[@]}; do
if [[ $check1 =~ $sample_id || $check2 =~ $sample_id ]]; then
echo "Controls ($sample_id) cannot be listed in contrast.csv - update and re-run"
exit 0
fi
done
}
function dryrun() {
# check essential files, load modules and do Dry-run
runcheck
# can add controlcheck if needed
if [ ! -d ${WORKDIR}/logs/dryrun/ ]; then mkdir ${WORKDIR}/logs/dryrun/; fi
if [ -f ${WORKDIR}/dryrun.log ]; then
modtime=$(stat ${WORKDIR}/dryrun.log |grep Modify|awk '{print $2,$3}'|awk -F"." '{print $1}'|sed "s/ //g"|sed "s/-//g"|sed "s/://g")
mv ${WORKDIR}/dryrun.log ${WORKDIR}/logs/dryrun/dryrun.${modtime}.log
fi
run "--dry-run"
}
function unlock() {
# check essential files, load modules and
# unlock the workdir if previous snakemake run ended abruptly
runcheck
run "--unlock"
}
function _exe_in_path() {
name_of_exe=$1
path_to_exe=$(which $name_of_exe 2>/dev/null)
if [ ! -x "$path_to_exe" ] ; then
err $path_to_exe NOT FOUND!
fi
}
function set_singularity_binds(){
# this functions tries find what folders to bind
# "Biowulf specific"
# assumes that config.yaml and samples.tsv in the WORKDIR are essential
# files with the most uptodate information
# required dos2unix in path
_exe_in_path dos2unix
echo "$PIPELINE_HOME" > ${WORKDIR}/tmp1
echo "$WORKDIR" >> ${WORKDIR}/tmp1
grep -o '\/.*' <(cat ${WORKDIR}/config.yaml ${WORKDIR}/samples.tsv)| \
dos2unix | \
tr '\t' '\n' | \
grep -v ' \|\/\/' | \
sort | \
uniq >> ${WORKDIR}/tmp1
grep gpfs ${WORKDIR}/tmp1|awk -F'/' -v OFS='/' '{print $1,$2,$3,$4,$5}' | \
grep "[a-zA-Z0-9]" | \
sort | uniq > ${WORKDIR}/tmp2
grep -v gpfs ${WORKDIR}/tmp1|awk -F'/' -v OFS='/' '{print $1,$2,$3}' | \
grep "[a-zA-Z0-9]" | \
sort | uniq > ${WORKDIR}/tmp3
while read a;do
readlink -f $a
done < ${WORKDIR}/tmp3 | grep "[a-zA-Z0-9]"> ${WORKDIR}/tmp4
binds=$(cat ${WORKDIR}/tmp2 ${WORKDIR}/tmp3 ${WORKDIR}/tmp4 | sort | uniq | tr '\n' ',')
rm -f ${WORKDIR}/tmp?
binds=$(echo $binds | awk '{print substr($1,1,length($1)-1)}')
SINGULARITY_BINDS="-B $EXTRA_SINGULARITY_BINDS,$binds"
}
function dag() {
runcheck
module load graphviz
snakemake -s $SNAKEFILE --configfile ${WORKDIR}/config/config.yaml --forceall --dag |dot -Teps > ${WORKDIR}/dag.eps
}
function testrun() {
# Run for a test run - this is an example and should be edited, as needed
check_essential_files
sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" ${PIPELINE_HOME}/.test/samples.test.tsv > $WORKDIR/config/samples.tsv
cp ${PIPELINE_HOME}/.test/contrasts.test.tsv $WORKDIR/config/contrasts.tsv
check_essential_files
dryrun
}
function printbinds(){
# set the singularity binds and print them
# singularity binds are /lscratch,/data/CCBR_Pipeliner,
# plus paths deduced from config.yaml and samples.tsv using
# set_singularity binds function
set_singularity_binds
echo $SINGULARITY_BINDS
}
function runlocal() {
# If the pipeline is fired up on an interactive node (with sinteractive),
# this function runs the pipeline
runcheck
set_singularity_binds
if [ "$SLURM_JOB_ID" == "" ];then err "runlocal can only be done on an interactive node"; fi
module load singularity
run "local"
}
function runslurm() {
# Submit the execution of the pipeline to the biowulf job scheduler (slurm)
runcheck
set_singularity_binds
run "slurm"
}
function _get_file_modtime() {
# get the modification time for a file
filename=$1
modtime=$(stat $filename|grep Modify|awk '{print $2,$3}'|awk -F"." '{print $1}'|sed "s/ //g"|sed "s/-//g"|sed "s/://g")
echo $modtime
}
function create_runinfo() {
# Create a runinfo.yaml file in the WORKDIR
if [ -f ${WORKDIR}/runinfo.yaml ];then
modtime=$(_get_file_modtime ${WORKDIR}/runinfo.yaml)
mv ${WORKDIR}/runinfo.yaml ${WORKDIR}/runinfo.yaml.${modtime}
fi
echo "Pipeline Dir: $PIPELINE_HOME" > ${WORKDIR}/runinfo.yaml
echo "Git Commit/Tag: $GIT_COMMIT_TAG" >> ${WORKDIR}/runinfo.yaml
userlogin=$(whoami)
username=$(finger $userlogin|grep ^Login|awk -F"Name: " '{print $2}')
echo "Login: $userlogin" >> ${WORKDIR}/runinfo.yaml
echo "Name: $username" >> ${WORKDIR}/runinfo.yaml
g=$(groups)
echo "Groups: $g" >> ${WORKDIR}/runinfo.yaml
d=$(date)
echo "Date/Time: $d" >> ${WORKDIR}/runinfo.yaml
}
function preruncleanup() {
# Cleanup function to rename/move files related to older runs to prevent overwriting them.
echo "Running..."
# check initialization
check_essential_files
cd $WORKDIR
## Archive previous run files
if [ -f ${WORKDIR}/snakemake.log ];then
modtime=$(_get_file_modtime ${WORKDIR}/snakemake.log)
mv ${WORKDIR}/snakemake.log ${WORKDIR}/stats/snakemake.${modtime}.log
if [ -f ${WORKDIR}/snakemake.log.HPC_summary.txt ];then
mv ${WORKDIR}/snakemake.log.HPC_summary.txt ${WORKDIR}/stats/snakemake.${modtime}.log.HPC_summary.txt
fi
if [ -f ${WORKDIR}/snakemake.stats ];then
mv ${WORKDIR}/snakemake.stats ${WORKDIR}/stats/snakemake.${modtime}.stats
fi
fi
nslurmouts=$(find ${WORKDIR} -maxdepth 1 -name "slurm-*.out" |wc -l)
if [ "$nslurmouts" != "0" ];then
for f in $(ls ${WORKDIR}/slurm-*.out);do mv ${f} ${WORKDIR}/logs/;done
fi
create_runinfo
}
function run() {
# RUN function
# argument1 can be:
# 1. local or
# 2. dryrun or
# 3. unlock or
# 4. slurm
if [ "$1" == "local" ];then
preruncleanup
snakemake -s $SNAKEFILE \
--directory $WORKDIR \
--printshellcmds \
--use-singularity \
--singularity-args "$SINGULARITY_BINDS" \
--use-envmodules \
--latency-wait 120 \
--configfile ${WORKDIR}/config.yaml \
--cores all \
--stats ${WORKDIR}/snakemake.stats \
2>&1|tee ${WORKDIR}/snakemake.log
if [ "$?" -eq "0" ];then
snakemake -s $SNAKEFILE \
--report ${WORKDIR}/runlocal_snakemake_report.html \
--directory $WORKDIR \
--configfile ${WORKDIR}/config.yaml
fi
elif [ "$1" == "slurm" ];then
preruncleanup
# if QOS is other than "global" and is supplied in the cluster.json file then add " --qos={cluster.qos}" to the
# snakemake command below
cat > ${WORKDIR}/submit_script.sbatch << EOF
#!/bin/bash
#SBATCH --job-name="CCBRPipeline"
#SBATCH --mem=10g
#SBATCH --partition="norm"
#SBATCH --time=96:00:00
#SBATCH --cpus-per-task=2
module load $PYTHON_VERSION
module load $SNAKEMAKE_VERSION
module load singularity
cd \$SLURM_SUBMIT_DIR
snakemake -s $SNAKEFILE \
--directory $WORKDIR \
--use-singularity \
--singularity-args "$SINGULARITY_BINDS" \
--use-envmodules \
--printshellcmds \
--latency-wait 120 \
--configfile ${WORKDIR}/config.yaml \
--cluster-config ${PIPELINE_HOME}/resources/cluster.yaml \
--cluster "sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}" \
-j 500 \
--rerun-incomplete \
--keep-going \
--stats ${WORKDIR}/snakemake.stats \
2>&1|tee ${WORKDIR}/snakemake.log
if [ "\$?" -eq "0" ];then
snakemake -s $SNAKEFILE \
--directory $WORKDIR \
--report ${WORKDIR}/runslurm_snakemake_report.html \
--configfile ${WORKDIR}/config.yaml
fi
bash <(curl https://github.com/raw/CCBR/Tools/master/Biowulf/gather_cluster_stats.sh 2>/dev/null) ${WORKDIR}/snakemake.log > ${WORKDIR}/snakemake.log.HPC_summary.txt
EOF
sbatch ${WORKDIR}/submit_script.sbatch
else # for unlock and dryrun
snakemake $1 -s $SNAKEFILE \
--directory $WORKDIR \
--use-envmodules \
--printshellcmds \
--latency-wait 120 \
--configfile ${WORKDIR}/config.yaml \
--cluster-config ${PIPELINE_HOME}/config/cluster.yaml \
--cluster "sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}" \
-j 500 \
--rerun-incomplete \
--keep-going \
--stats ${WORKDIR}/snakemake.stats
fi
}
function reset() {
# Delete the workdir and re-initialize it
echo "Working Dir: $WORKDIR"
if [ ! -d $WORKDIR ];then err "Folder $WORKDIR does not exist!";fi
echo "Deleting $WORKDIR"
rm -rf $WORKDIR
echo "Re-Initializing $WORKDIR"
init
}
function main(){
# Main function which parses all arguments
if [ $# -eq 0 ]; then usage && exit 1; fi
for i in "$@"; do
case $i in
-m=*|--runmode=*)
RUNMODE="${i#*=}"
;;
-w=*|--workdir=*)
WORKDIR="${i#*=}"
;;
*)
err "Unknown argument!" # unknown option
;;
esac
done
WORKDIR=$(readlink -f "$WORKDIR")
echo "Working Dir: $WORKDIR"
case $RUNMODE in
init) init && exit 0;;
dryrun) dryrun && exit 0;;
unlock) unlock && exit 0;;
run) runslurm && exit 0;;
runlocal) runlocal && exit 0;;
reset) reset && exit 0;;
dry) dryrun && exit 0;; # hidden option
local) runlocal && exit 0;; # hidden option
reconfig) reconfig && exit 0;; # hidden option for debugging
printbinds) printbinds && exit 0;; # hidden option
*) err "Unknown RUNMODE \"$RUNMODE\"";;
esac
}
# call the main function
main "$@"