view README.rst @ 4:4687ecf0eb2d draft

planemo upload for repository commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
author iuc
date Mon, 22 Jan 2018 11:26:13 -0500
parents bc4e467da875
children 3cdcd5753218
line wrap: on
line source

Trinity memory usage

As described on the official Trinity website
`FAQ <>`_,
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). -->
            <plugin id="local" type="runner" load="" workers="4"/>
            <handler id="main"/>
            <destination id="local" runner="local">
                <env id="GALAXY_MEMORY_MB">1G</env>