the shell must be specified last

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index e30372ac899cf9ff2779409a5a5ac2b34a6e1296..8e207f3a2af315a8a86a937776c1c5db806b418d 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -1,43 +1,44 @@
 #!/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 $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 ${SRR}.bam
+    module load samtools/1.0;
+    (cd "${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 $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 "$FROM_SRR_SRR";
+    (cd "$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";