Mercurial > repos > pjbriggs > trimmomatic
changeset 2:a60283899c6d draft
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
| author | pjbriggs |
|---|---|
| date | Wed, 22 Apr 2015 09:36:27 -0400 |
| parents | 2bd7cdbb6228 |
| children | f8a9a5eaca8a |
| files | README.rst trimmomatic.xml |
| diffstat | 2 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- a/README.rst Tue Dec 09 09:41:33 2014 -0500 +++ b/README.rst Wed Apr 22 09:36:27 2015 -0400 @@ -15,8 +15,9 @@ Automated installation ====================== -Installation via the Galaxy Tool Shed will take of installing the tool wrapper and -the trimmomatic program and data, and setting the appropriate environment variables. +Installation via the Galaxy Tool Shed will take care of installing the tool wrapper +and the trimmomatic program and data, and setting the appropriate environment +variables. Manual Installation =================== @@ -57,6 +58,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use + at runtime (default is 6). 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files into the XML wrapper. 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
--- a/trimmomatic.xml Tue Dec 09 09:41:33 2014 -0500 +++ b/trimmomatic.xml Wed Apr 22 09:36:27 2015 -0400 @@ -1,12 +1,12 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.32.1"> +<tool id="trimmomatic" name="Trimmomatic" version="0.32.2"> <description>flexible read trimming tool for Illumina NGS data</description> <command interpreter="bash">trimmomatic.sh -mx8G -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar #if $paired_end.is_paired_end - PE -threads 6 -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired + PE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired #else - SE -threads 6 -phred33 $fastq_in $fastq_out + SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out #end if ## ILLUMINACLIP option #if $illuminaclip.do_illuminaclip