Mercurial > repos > pjbriggs > trimmomatic

view trimmomatic_macros.xml @ 14:0fb869e9dee6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to Trimmomatic 0.38.
author pjbriggs
date Mon, 08 Jul 2019 06:07:07 -0400
parents 4fe90ae30670
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>