Mercurial > repos > pjbriggs > trimmomatic
changeset 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 | 898b67846b47 |
| children | 32f1f56bd970 |
| files | README.rst trimmomatic.xml trimmomatic_macros.xml |
| diffstat | 3 files changed, 15 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/README.rst Mon Jul 08 07:09:10 2019 -0400 +++ b/README.rst Thu Mar 26 04:52:47 2020 -0400 @@ -46,9 +46,9 @@ <tool file="trimmomatic/trimmomatic.xml" /> -You will also need to install trimmomatic 0.36: +You will also need to install trimmomatic 0.38: -- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip +- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip The tool wrapper uses the following environment variables in order to find the appropriate files: @@ -71,6 +71,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is + supported across both Linux and MacOS platforms. 0.38.0 - Update to Trimmomatic 0.38. 0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` and ``fastqsolexa`` input types @@ -117,6 +119,8 @@ support for gz compressed FastQ files. Charles Girardot (@cgirardot) and Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. Matthias Bernt (@bernt-matthias) added log and trimlog output. +Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform +support across Linux and MacOS. Developers ==========
--- a/trimmomatic.xml Mon Jul 08 07:09:10 2019 -0400 +++ b/trimmomatic.xml Thu Mar 26 04:52:47 2020 -0400 @@ -1,10 +1,16 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.38.0"> +<tool id="trimmomatic" name="Trimmomatic" version="0.38.1"> <description>flexible read trimming tool for Illumina NGS data</description> <macros> <import>trimmomatic_macros.xml</import> </macros> <requirements> <requirement type="package" version="0.38">trimmomatic</requirement> + <!-- + Coreutils required for 'readlink -e' work across platforms + See similar fix for snpSift + https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9 + --> + <requirement type="package" version="8.25">coreutils</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ @CONDA_TRIMMOMATIC_JAR_PATH@ &&
--- a/trimmomatic_macros.xml Mon Jul 08 07:09:10 2019 -0400 +++ b/trimmomatic_macros.xml Thu Mar 26 04:52:47 2020 -0400 @@ -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 -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> + <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> </macros>