Trinity-Teaching
Category
Bioinformatics
Program On
Teaching
Version
2.6.6
Author / Distributor
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 loads the module with
ml Trinity/2.6.6-foss-2016b
Here is an example of a shell script, sub.sh, to run on at 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
Installation
Source code is obtained from Trinity
System
64-bit Linux