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view trimmomatic_macros.xml @ 7:6eeacf19a38e draft

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Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
author pjbriggs
date Tue, 21 Mar 2017 08:42:05 -0400
parents f80107cdc406
children 51b771646466
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<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 -e \$(which trimmomatic))); fi</token>
  <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token>
</macros>