Mercurial > repos > pjbriggs > trimmomatic
annotate 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 |
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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).
pjbriggs
parents:
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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).
pjbriggs
parents:
diff
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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).
pjbriggs
parents:
diff
changeset
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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).
pjbriggs
parents:
diff
changeset
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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).
pjbriggs
parents:
diff
changeset
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5 --> |
14
d94aff5ee623
Version 0.38.1: add coreutils as dependency to fix tool issues with 'readlink -e' 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 'readlink -e' across platforms.
pjbriggs
parents:
12
diff
changeset
|
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> |
5
f80107cdc406
Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff
changeset
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8 </macros> |