Mercurial > repos > pjbriggs > trimmomatic
view trimmomatic_macros.xml @ 13:4fe90ae30670 draft
Uploaded fix from Marius van den Beek (make readlink more portable)
author | pjbriggs |
---|---|
date | Mon, 17 Dec 2018 04:33:20 -0500 |
parents | b0315888eb4d |
children | d300b1888cef |
line wrap: on
line source
<macros> <!-- Set the path for the trimmomatic JAR and data files Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13 --> <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi</token> <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -f \$(which trimmomatic)))/adapters; fi</token> </macros>