OrthoFinder-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.1.2

Author / Distributor

OrthoFinder

Description

"OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format." More details are at OrthoFinder

Running Program

The last version of this application is at /usr/local/apps/gb/orthofinder/2.1.2

To use this version, please load the module with

ml orthofinder/2.1.2 

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

#!/bin/bash
#SBATCH --job-name=j_OrthoFinder
#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=OrthoFinder.%j.out
#SBATCH --error=OrthoFinder.%j.err

cd $SLURM_SUBMIT_DIR
ml orthofinder/2.1.2
orthofinder.py [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 orthofinder/2.1.2 
orthofinder.py  -h
[https://github.com/davidemms/OrthoFinder OrthoFinder]

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Installation

Source code is obtained from OrthoFinder

System

64-bit Linux