reserve 32GB of ram

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 7de768ae2d85a773a8cc198f819e7f871605de20..82e4ae9c3d3f860033435416d481100612876fa5 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -1,8 +1,7 @@
 #!/bin/bash
-# PBS -M id -un
 
 CORES=8
-MAX_MEM=32
+MAX_MEM="32GB"
 
 
 function actually_run_the_alignment {
@@ -29,7 +28,7 @@ function set_up_the_run {
     (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"    
 };