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trinity-software

Trinity

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Information

Usage

See versions of trinity which are available:

$ module avail trinity

Load one version into your environment and run it:

$ module load trinity/v2.6.6
$ Trinity

Notes about running Trinity:

  • Please use the −−full_cleanup option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final fasta results
  • Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please direct the output from these jobs to a directory inside /var/scratch instead of your home folder.
  • For example:
  • #!/usr/bin/env bash
    #SBATCH -p highmem
    #SBATCH -J trinity
    #SBATCH -n 8
    
    module load trinity/v2.6.6
    
    # create and change to a working directory on the compute node
    export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
    mkdir -p $WORKDIR
    cd $WORKDIR
    
    # match CPUs to amount requested in SBATCH options!
    Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 --full_cleanup

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.6.6/Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz
$ tar xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz
$ cd Trinityrnaseq-v2.6.6
$ make
$ make plugins
$ sudo yum install numpy
$ sudo mkdir /export/apps/trinity/v2.6.6
$ make test_trinity
$ sudo cp -r . /export/apps/trinity/v2.6.6

Consult the installing Trinity guide in the documentation, although it misses some dependencies!

trinity-software.txt · Last modified: 2018/03/27 19:00 by aorth