trinity-software
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Table of Contents
Trinity
Trinity assembles transcript sequences from Illumina RNA-Seq data.
Information
- Version: v2.0.3
- Added: February, 2014
Usage
See versions of trinity which are available
module avail trinity
Note: Trinity creates millions of small files – which causes problems on the HPC storage server – so you must direct output from these jobs to /var/scratch instead of your home folder. For example:
#!/bin/env bash #SBATCH -p highmem #SBATCH -J trinity #SBATCH -n 10 module load trinity/v2.0.3 module load bowtie/1.1.1 module load samtools/1.2 # cd to working dir just in case export WORKDIR=$SLURM_JOBID 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 10 --output trinity-fish2
Installation
Notes from the sysadmin during installation:
$ cd ~/src $ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz $ tar xf v2.0.3.tar.gz $ cd trinityrnaseq-2.0.3 $ sudo mkdir /export/apps/trinity/v2.0.3 $ sudo chown aorth /export/apps/trinity/v2.0.3 $ cp -r * /export/apps/trinity/v2.0.3 $ scl enable devtoolset-2 bash $ make $ make plugins $ sudo chown -R root:root /export/apps/trinity/v2.0.3
trinity-software.1426865550.txt.gz · Last modified: 2015/03/20 15:32 by aorth