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;
13 fastq-dump ${FROM_SRR_SRR}.sra;
14 bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
15 samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
16 cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
17 rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
21 function set_up_the_run {
25 export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
26 mkdir -p "$FROM_SRR_SRR";
29 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;
31 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"
35 if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
36 if [ -z "$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";