Trinity-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.6.6

Author / Distributor

Trinity

Description

"Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads." More details are at Trinity

Running Program

The last version of this application is at /usr/local/apps/eb/Trinity/2.6.6-foss-2016b

To use this version, please load the module with

ml Trinity/2.6.6-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_Trinity
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Trinity.%j.out

cd $SLURM_SUBMIT_DIR
ml Trinity/2.6.6-foss-2016b
singularityexec/usr/local/singularity-images/trinity-2.5.1--0.simgTrinity [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml Trinity/2.6.6-foss-2016b 
singularityexec/usr/local/singularity-images/trinity-2.5.1--0.simgTrinity singularityexec/usr/local/singularity-images/trinity-2.5.1--0.simgTrinity --show_full_usage_info

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Installation

Source code is obtained from Trinity

System

64-bit Linux