Mercurial > repos > artbio > trinity
diff README.rst @ 0:b3fe7c4ca5aa draft default tip
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
author | artbio |
---|---|
date | Sat, 17 Mar 2018 17:43:58 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sat Mar 17 17:43:58 2018 -0400 @@ -0,0 +1,30 @@ +Trinity memory usage +==================== + +As described on the official Trinity website +`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, +trinity requires a large amount of memory to perform the assembly: "roughly +~1G of RAM per 1M reads to be assembled" + +By default, this tool is configured to limit the memory consumption to 1G. +You might need to lower this limit if the machine(s) executing the jobs have less memory available. +If you have a lot of reads to assemble and a machine with enough memory, you can increase it. +In both cases, you can set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file:: + + <?xml version="1.0"?> + <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> + <job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"> + <env id="GALAXY_MEMORY_MB">1G</env> + </destination> + </destinations> + </job_conf> + +