====== Trinity ======
Trinity assembles transcript sequences from Illumina RNA-Seq data.

===== Information =====

  * Latest Version: v2.11.0
  * Added: March, 2015
  * Updated: October, 2020
  * Link: https://trinityrnaseq.github.io

===== Usage =====
See versions of trinity which are available:
<code>$ module avail trinity</code>

Load one version into your environment and run it:
<code>$ module load trinity/v2.11.0
$ Trinity</code>

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:
  * <code>#!/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</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz
$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz
$ cd trinityrnaseq-v2.11.0
$ sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
$ make
$ make plugins
$ sudo yum install python36-numpy.x86_64
$ sudo mkdir -p /export/apps/trinity/v2.11.0
$ sudo cp -r . /export/apps/trinity/v2.11.0
$ export TRINITY_HOME=/export/apps/trinity/v2.11.0
$ module load samtools/1.9 salmon/1.3.0 bowtie2/2.3.4.1 jellyfish/2.3.0
$ cd sample_data/test_Trinity_Assembly
$ ./runMe.sh</code>

Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation.