# HG changeset patch
# User dvanzessen
# Date 1563785956 14400
# Node ID cb60ea3f8f62588c4a47070d01f47384717ead1c
# Parent  34eab86b26ba49a2278a8b4d43fd76cfe806270d
Uploaded

diff -r 34eab86b26ba -r cb60ea3f8f62 bcbio-nextgen.xml
--- a/bcbio-nextgen.xml	Mon Jul 22 04:56:23 2019 -0400
+++ b/bcbio-nextgen.xml	Mon Jul 22 04:59:16 2019 -0400
@@ -1,6 +1,6 @@
 <tool id="bcbio-nextgen" name="BCBio" version="0.1.0">
     <command detect_errors="exit_code"><![CDATA[
-        PATH="/bcbio/tool_dir/bin:/bcbio/anaconda/bin:\$PATH" && 
+        PATH="\$BCBIO_DIRECTORY/tool_dir/bin:\$BCBIO_DIRECTORY/anaconda/bin:\$PATH" && 
         mkdir $everything_else.files_path && 
         cd $everything_else.files_path &&
         python $__tool_directory__/script.py --workdir `pwd` --output-dir `pwd`/output --template $main --output-conf `pwd`/config.yaml
@@ -10,7 +10,7 @@
         #for $i, $sample in enumerate( $samples )
             --input $sample.forward:$sample.reverse:$sample.phenotype
         #end for
-        && bcbio_nextgen.py /bcbio/galaxy/bcbio_system.yaml `pwd`/config.yaml && 
+        && bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml && 
         zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
         python $__tool_directory__/make_html.py --input-dir $everything_else.files_path --root-html $everything_else
     ]]></command>