#!/bin/bash
-# PBS -M id -un
CORES=8
-MAX_MEM=32
+MAX_MEM="18GB"
+set -e;
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 $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 ${FROM_SRR_SRR}.bam;
+ module load samtools/1.0;
+ (cd "${FROM_SRR_SRR}";
+ 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;
rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
};
function set_up_the_run {
- FROM_SRR_SRR=$1
- FROM_SRR_REF=$2
- FROM_SRR_GTF=$3
+ FROM_SRR_SRR="$1"
+ FROM_SRR_REF="$2"
+ FROM_SRR_GTF="$3"
export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
- 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;
+ mkdir -p "$FROM_SRR_SRR";
+ (cd "$FROM_SRR_SRR";
+ 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"
+ 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"
};
-if [ -z "$1" ] || [ -z "$2"] || [ -z "$3" ]; then
- if [ -z "$FROM_SRR_SRR" ]; then
+if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
+ if [ -n "$FROM_SRR_SRR" ]; then
actually_run_the_alignment;
exit 0;
fi;
else
- set_up_the_run;
+ set_up_the_run "$1" "$2" "$3";
exit 0;
fi;
echo "You need to give an SRR, REF, and GTF on the command line";