annotate README.rst @ 11:aed859a021c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 482fb46ba8d588f2294e21829a0904809b0ec3f1

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>