X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fpkm_from_srr;h=bcb72bdbb381dd75d9d9802a2e927755e7389040;hb=7f58d05b94057af5e00aa0812302fe1b4e956876;hp=e30372ac899cf9ff2779409a5a5ac2b34a6e1296;hpb=85b7c5cb2963238e3b4de1bc8228130eb4295e97;p=uiuc_igb_scripts.git

diff --git a/fpkm_from_srr b/fpkm_from_srr
index e30372a..bcb72bd 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -9,12 +9,12 @@ 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
+    (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;
+     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
     );
 };
 
@@ -23,15 +23,16 @@ function set_up_the_run {
     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;
+    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;
     );
     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 "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
     if [ -z "$FROM_SRR_SRR" ]; then
         actually_run_the_alignment;
         exit 0;