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 1.8.17 with PASA pipeline with MySQL support is installed as an Apptainer container in /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/ . The image name is funannotate-1.8.17-mysql-production.sif.

To use this version of Funannotate in a batch job, please follow these setup steps in your current job working directory before submitting a batch job:

cp /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/*.sh .
cp -r /apps/singularity-images/funannotate-1.8.17-MySQL-PASA/pasa_conf .

Note:

1. Running the first cp command above will copy three MySQL config scripts: 1_init.sh, 2_create_user_and_db.sh, and 3_cleanup.sh to your current job working directory. It will also copy a PASA config folder pasa_conf to your current location.
2. Running the second cp command above will copy a sample job submission script sub.sh to your current working directory.

Below is the sample job submission script sub.sh, to run a batch job using 80 CPU cores on the batch partition:

#!/bin/bash
#SBATCH --job-name=funannotate-mysql
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=80
#SBATCH --mem=80gb
#SBATCH --time=48:00:00
#SBATCH --output=log.%j.out
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu

cd $SLURM_SUBMIT_DIR

# Initialize and start MySQL in the container

./1_init.sh && ./2_create_user_and_db.sh

# Verify the installation of dependencies and show their versions (optional)

apptainer exec instance://funannotate-mysql /bin/bash -c "source activate /opt/funannotate && funannotate check --show-versions"

# Run a full test with PASA pipeline with MySQL support. You can run your own funannotate command line here.

apptainer exec instance://funannotate-mysql /bin/bash -c "source activate /opt/funannotate && funannotate test -t all --cpus 80"

# Clean up on the compute node by shutting down MySQL

./3_cleanup.sh

Note:

1. In the real submission script, at least all the above underlined values in Slurm headers need to be reviewed or to be replaced by the proper values.
2. In the real submission script, the above the funannotate command lines in bold font can be replaced by your own funannotate command lines.

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

https://funannotate.readthedocs.io/en/latest/
https://github.com/PASApipeline/PASApipeline/wiki/setting-up-pasa-mysql

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Installation

Source code is obtained from https://github.com/nextgenusfs/funannotate

System

64-bit Linux