Rsem

Program description:
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Versions:

Name: rsem
Version: 1.2.18
Platform: x86_64
Category: Applications/Engineering
URL http://deweylab.biostat.wisc.edu/rsem/

Below is how to load the module into the software:
Module loading reference

Sample SLURM runtime script:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=4gb
#SBATCH --time=01:00:00

# Set paths or load appropriate modules
module load rsem/1.2.31

# Set the $TMPDIR variable
export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID

# We set application variables
export SCR=${TMPDIR}

# We set auxiliary variables
INPUT_DIR="exp"
INPUT_DIR2="ref"
OUTPUT_DIR="output"


# Create a temporary directory
mkdir -p ${TMPDIR}/${INPUT_DIR}
mkdir -p ${TMPDIR}/${INPUT_DIR2}

echo ${TMPDIR}
ls -la ${TMPDIR}

# Copy the input data to the directory pointed to by the $TMPDIR variable
cp -r ${SLURM_SUBMIT_DIR}/${INPUT_DIR} ${TMPDIR}
cp -r ${SLURM_SUBMIT_DIR}/${INPUT_DIR2} ${TMPDIR}

echo ${TMPDIR}
ls -la ${TMPDIR}

# Go to the $TMPDIR directory
cd $TMPDIR

# Header

cat << EOF
-------------------------------------------------- ---------------

Start of calculations [$(date)]
EOF

EOF

# We do the calculations
rsem-calculate-expression -p 24 --paired-end --bam --estimate-rspd
--append-names --output-genome-bam $INPUT_DIR/LPS_6h.bam $INPUT_DIR2/mouse_ref $INPUT_DIR/LPS_6h

# Footer
cat << EOF
-------------------------------------------------- ---------------

End of calculations [$(date)].

-------------------------------------------------- ---------------
EOF

# We finish the calculations, copy the contents of the $TMPDIR/output directory
# to the directory from which the job was queued.
mkdir $SLURM_SUBMIT_DIR/${OUTPUT_DIR}
cp -r $TMPDIR/* $SLURM_SUBMIT_DIR/${OUTPUT_DIR}/

# Clear working directory
rm -rf $TMPDIR

Example input: