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Repository trinity_align_and_estimate_abundance
Owner: iuc
Synopsis: Align reads and estimate abundance (from the Trinity tool suite)
Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
Type: unrestricted
Revision: 22:2fb4ee002432
This revision can be installed: True
Times cloned / installed: 1469

Repository README files - may contain important installation or license information

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.

This tool uses the GALAXY_MEMORY_MB environmental variable to limit the its memory usage. If you use a supported cluster type, you just need to limit the memory in the destination section of the job_conf.xml file to the amount of available memory (in MB), for example with a Slurm cluster:

<destination id="cluster_high_mem" runner="slurm
    <param id="nativeSpecification">--mem=1024</param>

If you cluster type does not support memory limit detection, you can also set manually the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file to the amount of available memory (in MB):

<?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">1024</env>

Contents of this repository

Name Description Version Minimum Galaxy Version
on a de novo assembly of RNA-Seq data 2.15.1+galaxy0 21.05

Transcriptomics - Tools for use in the study of Transcriptomics.
RNA - Utilities for RNA