--- /dev/null
+#!/bin/bash
+# PBS -M id -un
+
+CORES=8
+MAX_MEM=32
+
+
+function actually_run_the_alignment {
+ 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
+ );
+};
+
+function set_up_the_run {
+ FROM_SRR_SRR=$1
+ 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;
+ );
+ 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
+ actually_run_the_alignment;
+ exit 0;
+ fi;
+else
+ set_up_the_run;
+ exit 0;
+fi;
+echo "You need to give an SRR, REF, and GTF on the command line";
+exit 1;
+