quote variables

diff --git a/fpkm_from_srr b/fpkm_from_srr
index bcb72bdbb381dd75d9d9802a2e927755e7389040..eabc970fb5bb151072b50bbbc548a0b14b0572a6 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -19,11 +19,11 @@ function actually_run_the_alignment {
 };
 
 function set_up_the_run {
-    FROM_SRR_SRR=$1
-    FROM_SRR_REF=$2
-    FROM_SRR_GTF=$3
+    FROM_SRR_SRR="$1"
+    FROM_SRR_REF="$2"
+    FROM_SRR_GTF="$3"
     export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
-    mkdir -p $FROM_SRR_SRR;
+    mkdir -p "$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;
@@ -38,7 +38,7 @@ if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
         exit 0;
     fi;
 else
-    set_up_the_run;
+    set_up_the_run "$1" "$2" "$3";
     exit 0;
 fi;
 echo "You need to give an SRR, REF, and GTF on the command line";