trinity.sbat

#!/bin/bash

####  preamble

#SBATCH --job-name=trinity

#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=1:00:00

#SBATCH --account=training


####  End preamble

#  Put your job commands here:

WDIR=$(pwd)

# Create temporary directory, which is removed at end of run
TEMP=$(mktemp -d)
if [ $? -ne 0 ]; then
	echo "can't create $TEMP ... exit"
	exit 1
fi

trap '/bin/rm -rf $TEMP; exit' EXIT

# Copy data to $TEMP
echo "Copying to $TEMP ..."
if ! cp reads.right.fq.gz reads.left.fq.gz $TEMP; then
	echo "can't copy reads.right/.left to $TEMP ... exit"
	exit 1
fi

if ! cd $TEMP; then
	echo "can't chdir to $TEMP ... exit"
	exit 1
fi

if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
    echo "Unzipping reads.right ..."
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
    echo "Unzipping reads.left ..."
    gunzip -c reads.left.fq.gz > reads.left.fq
fi

# Run Trinity
echo "Running Trinity ..."
OUTFILE=trinity_out_dir.$(date +%F-%T)
mkdir $OUTFILE
echo + Trinity --seqType fq --max_memory 2G \
	--left reads.left.fq.gz \
	--right reads.right.fq.gz \
	--SS_lib_type RF \
	--output $OUTFILE \
	--CPU ${SLURM_CPUS_PER_TASK:-1}

# Save results
echo "Saving results from $TEMP/$OUTFILE to $WDIR ..."
if ! cp -ar $TEMP/$OUTFILE $WDIR; then
	echo "can't copy results to $WDIR ... exit"
	exit 1
fi

# Clean up /tmp
/bin/rm -rf $TEMP