From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 16:21:57 +0000 (-0700)
Subject: fix wrong SRR variable name
X-Git-Url: https://git.donarmstrong.com/?p=uiuc_igb_scripts.git;a=commitdiff_plain;h=6eda7b21639ec4a10d08e7de149d08f60d623504

fix wrong SRR variable name
---

diff --git a/fpkm_from_srr b/fpkm_from_srr
index eabc970..dab329d 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -26,7 +26,7 @@ function set_up_the_run {
     mkdir -p "$FROM_SRR_SRR";
     set -e;
     (cd $FROM_SRR_SRR;
-     wget -O ${FROM_SRR_SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra;
+     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;
     );
     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"    
 };