OrthoFinder-Teaching
Category
Bioinformatics
Program On
Teaching
Version
2.1.2
Author / Distributor
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
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 orthofinder.py -h [https://github.com/davidemms/OrthoFinder OrthoFinder]
Installation
Source code is obtained from OrthoFinder
System
64-bit Linux