Funannotate

Introduction

Funannotate is a genome prediction, annotation, and comparison software package.

For more information, please check:
Docker hub: https://hub.docker.com/r/nextgenusfs/funannotate
Home page: https://github.com/nextgenusfs/funannotate Note: For some steps, Funannotate needs to trains AUGUSTUS, i.e. writes species specific parameter files. Funannotate needs writing access to the configuration directory of AUGUSTUS that contains such files. This installation comes with a stub of AUGUSTUS coniguration files, but you must copy them out from the container into a location where you have write permissions. A helper command ‘copy_augustus_config’ is provided to simplify the task. Follow the procedure below to put the config files in your scratch space: $ mkdir -p $RCAC_SCRATCH/augustus $ copy_augustus_config $RCAC_SCRATCH/augustus $ export AUGUSTUS_CONFIG_PATH$RCAC_SCRATCH/augustus/config

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

v1.8.17, 1.8.10, 1.8.13, 1.8.15

BELL

v1.8.17, 1.8.10, 1.8.13, 1.8.15

GAUTSCHI

v1.8.17, 1.8.10, 1.8.13, 1.8.15

NEGISHI

v1.8.17, 1.8.10, 1.8.13, 1.8.15

SCHOLAR

1.8.10, 1.8.13

Commands

  • funannotate

Module

You can load the modules by:

module load biocontainers
module load funannotate

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run funannotate on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=funannotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers funannotate

# Your funannotate workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=funannotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers funannotate

# Your funannotate workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=funannotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers funannotate

# Your funannotate workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=funannotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers funannotate

# Your funannotate workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=funannotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers funannotate

# Your funannotate workflow...