Mercurial > repos > elixir-it > covacs_annovar

changeset 3:714413403c9a draft default tip

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Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:32:16 -0400
parents 40db0c5e3310
children
files covacs_annovar.xml mv_untar_annovar.sh
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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.
 
--- 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 &&