Mercurial > repos > pjbriggs > trimmomatic

diff trimmomatic_macros.xml @ 5:b0315888eb4d draft

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Test for version which is compatible with conda dependency resolver.
author pjbriggs
date Fri, 09 Dec 2016 12:17:15 -0500
parents
children 4fe90ae30670
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_macros.xml	Fri Dec 09 12:17:15 2016 -0500
@@ -0,0 +1,8 @@
+<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>