module load sratoolkit/2.3.5-2;
module load bwa/0.7.10;
module load cufflinks/2.2.1;
- (cd $SRR;
- fastq-dump ${SRR}.sra;
- bwa mem -t ${CORES} $REF ${SRR}.fastq.gz | samtools view -b -o ${SRR}.bam;
- samtools sort ${SRR}.bam -o ${SRR}.sorted.bam -T temp
- cufflinks -p ${MAX_MEM} -G $GTF ${SRR}.sorted.bam;
- rm -f ${SRR}.fastq.gz ${SRR}.bam
+ (cd $FROM_SRR_SRR;
+ fastq-dump ${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;
+ rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
);
};
FROM_SRR_REF=$2
FROM_SRR_GTF=$3
export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
- mkdir -p $SRR;
- (cd $SRR;
- wget -O ${SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${SRR:0:6}/${SRR}/${SRR}.sra;
+ mkdir -p $FROM_SRR_SRR;
+ set -e;
+ (cd $FROM_SRR_SRR;
+ wget -O ${FROM_SRR_SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${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"
};