Mercurial > repos > pjbriggs > trimmomatic
changeset 7:6eeacf19a38e draft
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
| author | pjbriggs |
|---|---|
| date | Tue, 21 Mar 2017 08:42:05 -0400 |
| parents | 141bba0e9a77 |
| children | 415a165d92bb |
| files | README.rst trimmomatic.xml |
| diffstat | 2 files changed, 19 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/README.rst Fri Feb 24 05:12:32 2017 -0500 +++ b/README.rst Tue Mar 21 08:42:05 2017 -0400 @@ -19,6 +19,19 @@ and the trimmomatic program and data, and setting the appropriate environment variables. +Controlling the available memory +================================ + +The default amount of memory avilable to trimmomatic is set to 8GB. +To change the default amount of memory you can set the environment variable +``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to +set this is in the job_conf.xml file. To change the available memory to 6GB, a +line like the below should be added: + +``<env id="_JAVA_OPTIONS">-Xmx6G</env>`` + +This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``. + Manual Installation =================== @@ -58,6 +71,9 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.36.3 - Fix naming of output collections. Instead of all outputs being called + "Trimmomatic on collection NN" these will now be called "Trimmomatic + on collection NN: paired" or "Trimmomatic on collection NN: unpaired". 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input the output will also be fastqsanger.gz. - Use $_JAVA_OPTIONS to customize memory requirements.
--- a/trimmomatic.xml Fri Feb 24 05:12:32 2017 -0500 +++ b/trimmomatic.xml Tue Mar 21 08:42:05 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.36.2"> +<tool id="trimmomatic" name="Trimmomatic" version="0.36.3"> <description>flexible read trimming tool for Illumina NGS data</description> <macros> <import>trimmomatic_macros.xml</import> @@ -175,12 +175,12 @@ <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> <filter>readtype['single_or_paired'] == 'se'</filter> </data> - <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired"> + <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired"> <filter>readtype['single_or_paired'] == "collection"</filter> <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/> <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/> </collection> - <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired"> + <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired"> <filter>readtype['single_or_paired'] == "collection"</filter> <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>