launch

#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
use Pod::Usage;
use Time::Piece;
use File::Basename;

my $NGS_PIPELINE;
my $mode = 'd';
my $time='20160415';
my $dataDir="";
my $sheet="samplesheet.json";
if (`dirname $0` =~ /^\./){
	$NGS_PIPELINE = `pwd`;
	chomp $NGS_PIPELINE;
}
else{
	$NGS_PIPELINE = `dirname $0`;
	chomp $NGS_PIPELINE;
}

if (`hostname` =~ /cn/ or `hostname` =~ /biowulf.nih.gov/){
	$dataDir="/data/khanlab/projects/DATA/";
}
elsif(`hostname` =~ /tghighmem/ or `hostname` =~ /tgcompute/ or `hostname` =~ /login01/){
	$dataDir="/projects/Clinomics/DATA/";
}

my $workDir="";
my $dryrun;
my $dag;
my $low_res;
my $help;
GetOptions(
		'dryrun'	=>\$dryrun,
		'dag'	=>\$dag,
		'low_res'	=>\$low_res,
		'mode|m=s'      =>\$mode,
		'datadir|d=s'   =>\$dataDir,
		'workdir|w=s'   =>\$workDir,
		'sheet|s=s'   	=>\$sheet,
		'help|h'      	=>\$help,
	  )or pod2usage();

$help and pod2usage ();

if (!$mode){
	print STDERR "ERROR: must specify '-mode'\n";
	print STDERR "\t Possible values are:\n";
	print STDERR "\t\td (development) Default\n";
	print STDERR "\t\tp (production)\n";
	exit;
}
if (!$dataDir){
        print STDERR "On biowulf the raw data is stored in /data/khanlab/projects/DATA/\n";
        print STDERR "On TGen the raw data is stored in /projects/Clinomics/DATA/\n";
	print STDERR "If your data is coming from somewhere else specify using this variable\n";
        exit;
}
if (!$workDir){
	print STDERR "This is required. Location where you would like to write results\n\n";
	exit;
}
if (!$sheet){
	print STDERR "By default it is assumed that samplesheet.json is present in working directory\n";
	print STDERR "if your samplesheet.json is not present in working directory, please give full path\n";
	print STDERR "relative paths are not full path\n";
	exit;
}

if ($mode eq 'p'){
	$time=`date +"%Y%m%d"`;
	chomp $time;
}
elsif($mode eq 'd'){
	$time=$time;
}
else{
	$time=$mode;
}
my $NOW=`echo \$(date +"%Y%m%d_%H%M%S")`;
chomp $NOW;
my $jobid;
my $sheet_name = basename($sheet, ".json");
my $time_limit = "6-00:00:00";
my $cluster_conf = "high";
if ($low_res) {
	$time_limit = "5-00:00:00";
	$cluster_conf = "low";
}
if (`hostname` =~ /cn/ or `hostname` =~ /biowulf.nih.gov/){
	if ($dryrun){
		my $dag_cmd = "";
		if ($dag) {
			$dag_cmd = "--dag | dot -Tsvg > dag.$mode.svg";
		}
		my $cmd = "(
		export TMP=$NOW
		export TIME=$time
		module load snakemake/5.24.1
		module load graphviz
		export NGS_PIPELINE=$NGS_PIPELINE
		export WORK_DIR=$workDir
		export DATA_DIR=$dataDir
		export ACT_DIR=\"/Actionable/\"
		export HOST=\"biowulf.nih.gov\"
		export SAMPLESHEET=$sheet_name
		export CLUSTER_CONF=$cluster_conf
		SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
		SAM_CONFIG=$sheet
		snakemake --directory \$WORK_DIR --snakefile \$SNAKEFILE --configfile \$SAM_CONFIG --dryrun -p -r --ri -R RNASeq split_vcf $dag_cmd
		rm -rf $workDir/ngs_pipeline_${sheet_name}_$NOW.csv
		)";
		print "$cmd\n";
		exec "$cmd";
	}
	else{
		`mkdir -p "$workDir/log/"`;
		`chmod g+rw "$workDir/log"`;
		$jobid = `sbatch -e $workDir/log/ngs-pipeline.%j.e -o $workDir/log/ngs-pipeline.%j.o --export=cluster_conf=$cluster_conf,time=$mode,ngs=$NGS_PIPELINE,dataDir=$dataDir,workDir=$workDir,sheet=$sheet,runTime=$NOW --cpus-per-task=1 --mem=2G --partition=ccr,norm --mail-type=TIME_LIMIT_90 --time=$time_limit $NGS_PIPELINE/submit_snakemake.sh`;
	}
}
elsif(`hostname` =~ /tghighmem/ or `hostname` =~ /tgcompute/ or `hostname` =~ /login01/){
	if ($dryrun){
		my $dag_cmd = "";
		if ($dag) {
			$dag_cmd = "--dag | dot -Tsvg > dag.$mode.svg";
		}
		my $cmd= "(
		export TMP=$NOW
		export TIME=$time
                module load snakemake/5.24.1
                module load graphviz
                export NGS_PIPELINE=$NGS_PIPELINE
                export WORK_DIR=$workDir
                export DATA_DIR=$dataDir
                export ACT_DIR=\"/Actionable/\"
                export HOST=\"login01\"
		export SAMPLESHEET=$sheet_name
                SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
                SAM_CONFIG=$sheet
                snakemake --directory \$WORK_DIR --snakefile \$SNAKEFILE --configfile \$SAM_CONFIG --dryrun -p -r --ri -R RNASeq $dag_cmd
		rm -rf $workDir/ngs_pipeline_${sheet_name}_$NOW.csv
		)";
		print "$cmd\n";
		exec "$cmd";	
	}
	else{
		`mkdir -p "$workDir/log/"`;
		`chmod g+rw "$workDir/log/"`;
		$jobid = `sbatchT -e $workDir/log/ngs-pipeline.%j.e -o $workDir/log/ngs-pipeline.%j.o --export=time=$mode,ngs=$NGS_PIPELINE,dataDir=$dataDir,workDir=$workDir,sheet=$sheet,runTime=$NOW --cpus-per-task=1 --mem=4G --partition=batch --time=08-00:00:00 $NGS_PIPELINE/submit_snakemake.sh`;
	}
}
else{
	print STDERR "This pipeline is not configured to run on this host `hostname`\n";
	print STDERR "Please change configuration files as well as Snakemake file to accomodate the same\n";
	die;
}


chomp $jobid;
print "$jobid\t$sheet\t$NGS_PIPELINE\t$workDir/ngs_pipeline_${sheet_name}_$NOW.log\n" if $jobid;

=head1 SYNOPSIS

 launch -mode d -datadir /projects/Clinomics/DATA/ -workdir /projects/Clinomics/Test_Run2 -s /projects/Clinomics/Test_Run2/SampleSheets/samplesheet.json
 ###############################################################
 Arguments: 

        -h, -help, --help Print this message.

        -m, -mode	This sets up the time in the patient directory, in production mode the time is dynamically decided, 
			 in dev mode a pre set time is used for debugging purposes.
			 if new libraries are secqueced from a case -m <previous Data> could be used as mode.
		Accpeted values:
			p =production mode <todays date>	
			d =development mode <preset date 20160415>
			<20160415> = to use this is caseID for the sample. this sould only be done with single subject json file

	-d, -datadir	On biowulf the raw data is stored in /data/khanlab/projects/DATA/
			  On TGen the raw data is stored in /projects/Clinomics/DATA/
			  If your data is coming from somewhere else specify using this variable
			  -datadir "/data/Clinomics/testData/"

	-w, -workdir	Working directory where all the results will be stored. there are defaults to be used specific to host.
	-s, -sheet 	A json file downloded from  https://fr-s-bsg-onc-d.ncifcrf.gov/onco.sandbox1/public/viewPatients/null/all/1 
			this dictates how the pipeline will ran.
				default name is samplesheet.json in working directory.
				if present somewhere else please give full path.
 ##############################################################

	##########################################
	#
	#	It is assumed that workdir contains the samplesheet.json
	#		if not the case use -s <full path of samplesheet.json>
	#
	##########################################
 	#
	#	DryRun
	#
	##########################################
	#
	#
	#	Biowulf
	#
		export TMP="20160415"
		export TIME="20160415"
		module load snakemake/5.24.1
                export NGS_PIPELINE="/data/Clinomics/Tools/ngs_pipeline-dev/"
                export WORK_DIR="`pwd`"
                export DATA_DIR="/data/khanlab/projects/DATA/"
                #export DATA_DIR="/data/Clinomics/DATA/"
                export ACT_DIR="/Actionable/"
                export HOST="biowulf.nih.gov"
                SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
                SAM_CONFIG=$WORK_DIR/samplesheet.json
		snakemake --directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --dryrun -p -r
	#
	#
	#	TGen
	#
		export TMP="20160415"
		export TIME="20160415"
                module load snakemake/5.24.1
                export NGS_PIPELINE="/projects/Clinomics/Tools/ngs_pipeline/"
                export WORK_DIR="`pwd`"
                export DATA_DIR="/projects/Clinomics/DATA/"
                export ACT_DIR="/Actionable/"
                export HOST="login01"
                SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
                SAM_CONFIG=$WORK_DIR/samplesheet.json
		snakemake --directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --dryrun -p -r                                  
	

	#Summary 
	#  snakemake --directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --summary
	
	# DRY Run with Print out the shell commands that will be executed
	#  snakemake --directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --dryrun -p -r

	#DAG 
	#  snakemake --directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --dag | dot -Tpng > dag.png

	#Rulegraph
	#  snakemake --directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG -n --forceall --rulegraph | dot -Tpng > Rulegraph.png

	# Mail Rulegraph and DAG to self
	#  echo DAG |mutt -s "DAG" -a dag.png -a Rulegraph.png -- patidarr@mail.nih.gov
	                                                                                                                      

 For questions or comments, please contact: Rajesh Patidar <rajesh.patidar@nih.gov>

=cut