Mercurial > repos > pjbriggs > trimmomatic

annotate trimmomatic_macros.xml @ 13:898b67846b47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated to Trimmomatic 0.38.
author pjbriggs
date Mon, 08 Jul 2019 07:09:10 -0400
parents 51b771646466
children d94aff5ee623
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
1 <macros>
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
2 <!--
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
3 Set the path for the trimmomatic JAR and data files
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
5 -->
12
51b771646466 Uploaded fix from Marius van den Beek (make readlink more portable)
pjbriggs
parents: 5
diff changeset
6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi</token>
51b771646466 Uploaded fix from Marius van den Beek (make readlink more portable)
pjbriggs
parents: 5
diff changeset
7 <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -f \$(which trimmomatic)))/adapters; fi</token>
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
8 </macros>