Mercurial > repos > pjbriggs > trimmomatic
comparison trimmomatic_macros.xml @ 14:d94aff5ee623 draft
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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| 13:898b67846b47 | 14:d94aff5ee623 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <!-- | 2 <!-- |
| 3 Set the path for the trimmomatic JAR and data files | 3 Set the path for the trimmomatic JAR and data files |
| 4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13 | 4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13 |
| 5 --> | 5 --> |
| 6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi</token> | 6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token> |
| 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> | 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> |
| 8 </macros> | 8 </macros> |