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| #!/bin/bash | |
| # module init required when running on non-OSG resources, and has to sourced | |
| # before set -e as sometimes it exits non-0 when a module environment is | |
| # already set up | |
| . /cvmfs/oasis.opensciencegrid.org/osg/sw/module-init.sh | |
| set -e | |
| module load java/8u25 | |
| module load sra/2.8.0 | |
| if [ "$#" -eq 4 ] ; then | |
| SRA_ID=$1 | |
| FORWARD=$2 | |
| REVERSE=$3 | |
| LAYOUT=$4 | |
| elif [ "$#" -eq 3 ] ; then | |
| SRA_ID=$1 | |
| FORWARD=$2 | |
| LAYOUT=$3 | |
| fi | |
| if [ $LAYOUT = "paired" ] ; then | |
| fastq-dump --split-files --gzip $SRA_ID | |
| mv ${SRA_ID}_1.fastq.gz $FORWARD | |
| mv ${SRA_ID}_2.fastq.gz $REVERSE | |
| echo | |
| ls -lh | |
| echo | |
| elif [ $LAYOUT = "single" ] ; then | |
| fastq-dump --gzip $SRA_ID | |
| mv ${SRA_ID}.fastq.gz $FORWARD | |
| echo | |
| ls -lh | |
| echo | |
| fi |