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annotate trimmomatic_macros.xml @ 14:d94aff5ee623 draft

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Version 0.38.1: add coreutils as dependency to fix tool issues with 'readlink -e' across platforms.
author pjbriggs
date Thu, 26 Mar 2020 04:52:47 -0400
parents 51b771646466
children 32f1f56bd970
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f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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1 <macros>
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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2 <!--
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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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).
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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).
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5 -->
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d94aff5ee623 Version 0.38.1: add coreutils as dependency to fix tool issues with &#39;readlink -e&#39; across platforms.
pjbriggs
parents: 12
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6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token>
d94aff5ee623 Version 0.38.1: add coreutils as dependency to fix tool issues with &#39;readlink -e&#39; across platforms.
pjbriggs
parents: 12
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7 <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token>
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f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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8 </macros>