8 function actually_run_the_alignment {
9 module load sratoolkit/2.3.5-2;
10 module load bwa/0.7.10;
11 module load cufflinks/2.2.1;
12 module load samtools/1.0;
13 (cd "${FROM_SRR_SRR}";
14 fastq-dump --gzip ${FROM_SRR_SRR}.sra;
15 bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam -;
16 samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
17 cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
18 rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
22 function set_up_the_run {
26 export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
27 mkdir -p "$FROM_SRR_SRR";
29 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 .;
31 qsub -q budget -v FROM_SRR_SRR,FROM_SRR_GTF,FROM_SRR_REF -S /bin/bash -d $(pwd) -m a -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"
35 if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
36 if [ -n "$FROM_SRR_SRR" ]; then
37 actually_run_the_alignment;
41 set_up_the_run "$1" "$2" "$3";
44 echo "You need to give an SRR, REF, and GTF on the command line";