configuration of vcfDir

vcfGenotypeLookup.bash : use -e to check for vcf dir / link existence; -x works in bash, and container has /bin/bash, but its -x doesn't work as expected
plantinformatics · Mar 23, 2023 · f489272 · f489272
1 parent d9cf889
commit f489272
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/lb4app/lb3app/scripts/vcfGenotypeLookup.bash b/lb4app/lb3app/scripts/vcfGenotypeLookup.bash
@@ -31,9 +31,9 @@ unused_var=${blastDir:=/mnt/data_blast/blast}
 unused_var=${vcfDir:=$blastDir/../vcf}
 # blastDir=tmp/blast
 vcfDir=tmp/vcf
-if [ ! -x $vcfDir -a -x $blastDir/vcf ]
+if [ ! -e "$vcfDir" -a -e "$blastDir/vcf" ]
 then
-  vcfDir=$blastDir/vcf
+  vcfDir="$blastDir/vcf"
 fi
 unused_var=${datasetIdDir:=$vcfDir/datasetId}