use rsync instead of wget

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index dab329d9ba2b526621346712a6867ecc0751937c..a7ab6e0a4ef9c03c818c9737f1c0a810cc7b87f8 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -26,14 +26,14 @@ function set_up_the_run {
     mkdir -p "$FROM_SRR_SRR";
     set -e;
     (cd $FROM_SRR_SRR;
-     wget -O ${FROM_SRR_SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${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 $(pwd) -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"    
 };
 
 
 if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
-    if [ -z "$FROM_SRR_SRR" ]; then
+    if [ -n "$FROM_SRR_SRR" ]; then
         actually_run_the_alignment;
         exit 0;
     fi;