module load sratoolkit/2.3.5-2;
module load bwa/0.7.10;
module load cufflinks/2.2.1;
+ module load samtools/1.0;
(cd $FROM_SRR_SRR;
- fastq-dump ${FROM_SRR_SRR}.sra;
+ fastq-dump --gzip ${FROM_SRR_SRR}.sra;
bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
mkdir -p "$FROM_SRR_SRR";
set -e;
(cd $FROM_SRR_SRR;
- wget -O ${FROM_SRR_SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra;
+ rsync -avP rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra;
);
qsub -q budget -v FROM_SRR_SRR,FROM_SRR_GTF,FROM_SRR_REF -S /bin/bash -d $(pwd) -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"
};
if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
- if [ -z "$FROM_SRR_SRR" ]; then
+ if [ -n "$FROM_SRR_SRR" ]; then
actually_run_the_alignment;
exit 0;
fi;