Mercurial > repos > pjbriggs > trimmomatic
view trimmomatic_macros.xml @ 7:6eeacf19a38e draft
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>