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launch
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#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
use Pod::Usage;
use Time::Piece;
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 $help;
GetOptions(
'dryrun' =>\$dryrun,
'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 (!$sheet){
print STDERR "Be default it is assumed that samplesheet.json is present in working directory\n";
print STDERR "if your samplesheet.json is not present in working directory, please give full path\n";
print STDERR "relative paths are not full path\n";
exit;
}
if ($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 $NOW;
if (`hostname` =~ /cn/ or `hostname` =~ /biowulf.nih.gov/){
if ($dryrun){
my $cmd = "(
export TMP=$NOW
export TIME=$time
module load snakemake/3.8.0
export NGS_PIPELINE=$NGS_PIPELINE
export WORK_DIR=$workDir
export DATA_DIR=$dataDir
export ACT_DIR=\"/Actionable/\"
export HOST=\"biowulf.nih.gov\"
SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
SAM_CONFIG=$sheet
snakemake --directory \$WORK_DIR --snakefile \$SNAKEFILE --configfile \$SAM_CONFIG --dryrun -p -r --ri -R RNASeq
rm -rf $workDir/ngs_pipeline_$NOW.csv
)";
print "$cmd\n";
exec "$cmd";
}
else{
`mkdir -p "$workDir/log/"`;
`sbatch -e $workDir/log/ngs-pipeline.e -o $workDir/log/ngs-pipeline.o --export=time=$mode,ngs=$NGS_PIPELINE,dataDir=$dataDir,workDir=$workDir,sheet=$sheet --cpus-per-task=1 --partition=ccr,norm --time=10-00:00:00 $NGS_PIPELINE/submit_snakemake.sh`;
}
}
elsif(`hostname` =~ /tghighmem/ or `hostname` =~ /tgcompute/ or `hostname` =~ /login01/){
if ($dryrun){
my $cmd= "(
export TMP=$NOW
export TIME=$time
module load snakemake/3.8.0
export NGS_PIPELINE=$NGS_PIPELINE
export WORK_DIR=$workDir
export DATA_DIR=$dataDir
export ACT_DIR=\"/Actionable/\"
export HOST=\"login01\"
SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
SAM_CONFIG=$sheet
snakemake --directory \$WORK_DIR --snakefile \$SNAKEFILE --configfile \$SAM_CONFIG --dryrun -p -r --ri -R RNASeq
rm -rf $workDir/ngs_pipeline_$NOW.csv
)";
print "$cmd\n";
exec "$cmd";
}
else{
`mkdir -p "$workDir/log/"`;
`sbatchT -e $workDir/log/ngs-pipeline.e -o $workDir/log/ngs-pipeline.o --export=time=$mode,ngs=$NGS_PIPELINE,dataDir=$dataDir,workDir=$workDir,sheet=$sheet --cpus-per-task=1 --partition=batch --time=10-00:00:00 $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;
}
=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/3.8.0
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 $SAM_CONFIG --dryrun -p -r
#
#
# TGen
#
export TMP="20160415"
export TIME="20160415"
module load snakemake/3.8.0
export NGS_PIPELINE="/projects/Clinomics/Tools/ngs_pipeline/"
export WORK_DIR="`pwd`"
export DATA_DIR="/projects/Clinomics/DATA/"
export ACT_DIR="/Actionable/"
export HOST="login01"
SNAKEFILE=$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