# HG changeset patch
# User elixir-it
# Date 1570005136 14400
# Node ID 714413403c9ae13426410fd8d66a8b01caa6abea
# Parent  40db0c5e33107ac78283c0bc0ec197bb8b2dac8a
Uploaded

diff -r 40db0c5e3310 -r 714413403c9a covacs_annovar.xml
--- a/covacs_annovar.xml	Wed Nov 21 04:21:06 2018 -0500
+++ b/covacs_annovar.xml	Wed Oct 02 04:32:16 2019 -0400
@@ -5,7 +5,7 @@
   </requirements>
   <command> <![CDATA[
        ### call the .sh to untar the package 
-	sh $__tool_directory__/mv_untar_annovar.sh &&
+	bash $__tool_directory__/mv_untar_annovar.sh &&
 
 	 ## Variant annotation; make sure to include entry in indexes table for build database.
 
diff -r 40db0c5e3310 -r 714413403c9a mv_untar_annovar.sh
--- a/mv_untar_annovar.sh	Wed Nov 21 04:21:06 2018 -0500
+++ b/mv_untar_annovar.sh	Wed Oct 02 04:32:16 2019 -0400
@@ -1,7 +1,7 @@
 #!/bin/bash
 # if the symbolic link is not present in the annovar conda virtual environment the script search for the tar.gz in the conda_prefix,
 # untar the archive and make a symbolic link to the $CONDA_PREFIX of the conda virtual environment
-if [[ ! -d $CONDA_PREFIX/annovar ]] ; then
+if [ ! -d $CONDA_PREFIX/annovar ] ; then
 	tar -zxvf $CONDA_PREFIX/../../annovar.*.tar.gz -C $CONDA_PREFIX/../../ &&
 	echo start untar &&
 	ln -s $CONDA_PREFIX/../../annovar $CONDA_PREFIX &&