add destination directory

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 9a310e51e956c560eab99e3bc15e50778ce0b225..34eb3049f3bc967f04584f688d4772b86e98b025 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -26,7 +26,7 @@ function set_up_the_run {
     export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
     mkdir -p "$FROM_SRR_SRR";
     (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"    
 };