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Running Maker on Hopper

MAKER is a genome annotation pipeline that is scalable and can be installed and run on Hopper. The following instructions have steps for installing Maker in your home directory on the cluster and running it. After completing the installation steps, a tutorial for Maker can be found on this page: Maker Tutorial. The examples in the tutorial were used to test the installed Maker.

Installing Maker in a python virtual environment with Miniconda3

  1. Download miniconda3:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  1. Install it in your preferred path:
 bash Miniconda3-latest-Linux-x86_64.sh -b -p $PWD/miniconda
  1. Activate base conda environment:
 source miniconda/bin/activate
 export PYTHONNOUSERSITE=true
  1. Download and create your virtual environment for maker using the environment yml file. This was generated from tests on the cluster so it should have all the necessary libraries. To download the environment.yml file maker_3.01.03_environment.yml use:

wget https://wiki.orc.gmu.edu/mkdocs/maker/maker_3.01.03_environment.yml
Then create the virtual environemnt with: 
conda env create -f maker_3.01.03_environment.yml
  1. You should now be able to activate it with: 
conda activate maker_3.01.03

and generate the control files:

maker -CTL

Running in batch mode with SLURM

Below is an example of a SLURM script (run.slurm) to run in this conda environment. You can modify the different SLURM parameters to match what you need:

Download the run.slurm script: 

wget https://wiki.orc.gmu.edu/mkdocs/maker/run.slurm

#!/bin/bash
#SBATCH --job-name=maker_test
#SBATCH --partition=normal
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=64
#SBATCH --output=maker_test_%j.out
#SBATCH --error=maker_test_%j.err
#SBATCH --mem=50GB
#SBATCH --time=0-12:00:00

### Load modules
module unload openmpi4
module load gnu10 openmpi

### Activate virtual environment
source /home/$USER/miniconda/bin/activate
source activate maker_3.01.03

### Set environment variables:
export LIBDIR=/home/$USER/miniconda/envs/maker_3.01.03/share/RepeatMasker/Libraries

### Execute program
mpiexec -n ${SLURM_NTASKS_PER_NODE} maker [OPTIONS]

Run this with the sbatch command:

sbatch run.slurm

If you ssh onto the node on which the jobs starts, you should see it now utilizes all the available cpus for maker. To see which nodes the job is running on, you can use the squeue command:

squeue --me