Mercurial > repos > pjbriggs > trimmomatic

annotate trimmomatic_macros.xml @ 14:0fb869e9dee6 draft

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Update to Trimmomatic 0.38.
author pjbriggs
date Mon, 08 Jul 2019 06:07:07 -0400
parents 4fe90ae30670
children d300b1888cef
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b0315888eb4d Test for version which is compatible with conda dependency resolver.
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1 <macros>
b0315888eb4d Test for version which is compatible with conda dependency resolver.
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2 <!--
b0315888eb4d Test for version which is compatible with conda dependency resolver.
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3 Set the path for the trimmomatic JAR and data files
b0315888eb4d Test for version which is compatible with conda dependency resolver.
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4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13
b0315888eb4d Test for version which is compatible with conda dependency resolver.
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5 -->
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4fe90ae30670 Uploaded fix from Marius van den Beek (make readlink more portable)
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6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi</token>
4fe90ae30670 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>
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b0315888eb4d Test for version which is compatible with conda dependency resolver.
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8 </macros>