stop immediately upon error

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 7de768ae2d85a773a8cc198f819e7f871605de20..9a310e51e956c560eab99e3bc15e50778ce0b225 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -1,9 +1,9 @@
 #!/bin/bash
-# PBS -M id -un
 
 CORES=8
-MAX_MEM=32
+MAX_MEM="32GB"
 
+set -e;
 
 function actually_run_the_alignment {
     module load sratoolkit/2.3.5-2;
@@ -25,11 +25,10 @@ function set_up_the_run {
     FROM_SRR_GTF="$3"
     export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
     mkdir -p "$FROM_SRR_SRR";
-    set -e;
     (cd $FROM_SRR_SRR;
      rsync -avP rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${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 $(pwd) -m ae -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"    
 };