X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fpkm_from_srr;h=34eb3049f3bc967f04584f688d4772b86e98b025;hb=d9e75281e8c6ce08d6f3e2d9e350cca877e7126a;hp=82e4ae9c3d3f860033435416d481100612876fa5;hpb=e3a076b12c9216f42d6b8ae13751696fa0f3cd52;p=uiuc_igb_scripts.git

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 82e4ae9..34eb304 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -3,6 +3,7 @@
 CORES=8
 MAX_MEM="32GB"
 
+set -e;
 
 function actually_run_the_alignment {
     module load sratoolkit/2.3.5-2;
@@ -24,9 +25,8 @@ 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;
+     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 $(pwd) -m ae -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"    
 };