Funannotate-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
1.8.17
Author / Distributor
https://github.com/nextgenusfs/funannotate https://funannotate.readthedocs.io/en/latest/
Description
"Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes." More details are at https://funannotate.readthedocs.io/en/latest/
Running Program
Version
To use this version, please load the module with
ml HISAT2/3n-20201216-gompi-2022a
To use version 2.2.1, please load the module with
ml HISAT2/2.2.1-gompi-2022a
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_HISAT2
#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=HISAT2.%j.out
#SBATCH --error=HISAT2.%j.err
cd $SLURM_SUBMIT_DIR
ml HISAT2/2.2.1-gompi-2022a
hisat2 [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 Sapelo2 for more information running jobs on the Sapelo2 cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
Installation
Source code is obtained from HISAT2
System
64-bit Linux