Mercurial > repos > dvanzessen > bcbio_nextgen_emc
changeset 3:cb60ea3f8f62 draft
Uploaded
author | dvanzessen |
---|---|
date | Mon, 22 Jul 2019 04:59:16 -0400 |
parents | 34eab86b26ba |
children | 7211d3a78fe0 |
files | bcbio-nextgen.xml |
diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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>