Mercurial > repos > pjbriggs > trimmomatic
changeset 12:51b771646466 draft
Uploaded fix from Marius van den Beek (make readlink more portable)
| author | pjbriggs |
|---|---|
| date | Mon, 17 Dec 2018 04:39:08 -0500 |
| parents | 59054f086eca |
| children | 898b67846b47 |
| files | trimmomatic_macros.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/trimmomatic_macros.xml Fri Oct 05 05:19:17 2018 -0400 +++ b/trimmomatic_macros.xml Mon Dec 17 04:39:08 2018 -0500 @@ -3,6 +3,6 @@ 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> + <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi</token> + <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -f \$(which trimmomatic)))/adapters; fi</token> </macros>