making consistent with dev version; adding in -V to nvcc command and updating dirs (d9e6c7bf) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+16 −8

Original line number	Diff line number	Diff line
		@@ -91,7 +91,7 @@ elif [ $isBCM -eq 1 ]
		then
		# Juicer directory, contains scripts/, references/, and restriction_sites/
		# can also be set in options via -D
		juiceDir="/storage/aiden/juicer/BioScripts/SLURM"
		juiceDir="/storage/aiden/juicer/"
		# default queue, can also be set in options via -q
		queue="mhgcp"
		queue_time="1200"
		@@ -100,13 +100,12 @@ then
		long_queue_time="3600"
		else
		isVoltron=1
		#source activate /gpfs0/biobuild/biobuilds-2016.04

		export PATH=/gpfs0/biobuild/biobuilds-2016.11/bin:$PATH
		# export PATH=$PATH:/usr/local/cuda/bin/
		unset MALLOC_ARENA_MAX
		# Juicer directory, contains scripts/, references/, and restriction_sites/
		# can also be set in options via -D
		juiceDir="/gpfs0/juicer/BioScripts/SLURM/"
		juiceDir="/gpfs0/juicer/"
		# default queue, can also be set in options
		queue="commons"
		# default long queue, can also be set in options
		@@ -833,13 +832,22 @@ then

		# merge the sorted files into one giant file that is also sorted. jid=`sbatch <<- MRGSRT \| egrep -o -e "\b[0-9]+$"

		if [ $isVoltron -eq 1 ]
		then
		sbatch_time="#SBATCH -t 10080"
		else
		sbatch_time="#SBATCH -t 1440"
		fi



		jid=`sbatch <<- EOF
		#!/usr/bin/bash
		#SBATCH -o $debugdir/fragmerge-%j.out
		#SBATCH -e $debugdir/fragmerge-%j.err
		#SBATCH --mem 256000
		#SBATCH -t 1440
		#SBATCH -p $queue
		${sbatch_time}
		#SBATCH -p $long_queue
		#SBATCH -c 8
		#SBATCH -J "${groupname}_fragmerge"
		${sbatch_wait}
		@@ -1125,13 +1133,13 @@ HIC30`
		echo "load: $load_gpu"
		${load_java}
		date
		nvcc
		nvcc -V
		if [ -f "${errorfile}" ]
		then
		echo "***! Found errorfile. Exiting."
		exit 1
		fi
		source ${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID
		${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID
		date
		HICCUPS`
		dependhiccups="afterok:$jid"

Admin message