Tabix

Program description:
Toolkit

Versions:

Name: tabix
Version: 0.2.6
Platform: x86_64
Category: Applications/Engineering
URL http://samtools.sourceforge.net/tabix.shtml

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 samtools
module load tabix

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

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

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


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

# Go to the $TMPDIR directory
cd $TMPDIR

# We do the calculations
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S2RawDataRep1.fastq.gz
bgzip byEncodeUwRepliSeqK562S2RawDataRep1.fastq.gz
tabix -p same byEncodeUwRepliSeqK562S2RawDataRep1.fastq.gz.gz

# 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: