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Install, setup, and run BEAST2 on Atlas HPC

8/23/24

Initiate Conda

1. Open a Shell

Open a shell on Atlas and navigate to your project directory.

2. Load the Miniconda3 Module

module load miniconda3

3. Initialize Conda

Initialize Conda to work with your shell:

conda init

4. Close and Reopen Your Shell

You may need to restart your shell session. Close your terminal window and open a new one.

Create Conda Environment

5. Create a New Conda Environment for BEAST2

Creating an environment helps manage dependencies. In the code below, replace beast2_env with any name of your choosing.

conda create -n beast2_env
  • When prompted, type Y to proceed with the environment creation.

6. Activate the Conda Environment

conda activate beast2_env

You should see the environment name prefixed in your shell prompt (before your username).

7. Configure Conda Channels

Add the necessary channels to install BEAST2 and its dependencies.

conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels defaults
conda config --show channels

You should see:

channels:
  - conda-forge
  - bioconda
  - defaults

Install BEAST2

8. Install BEAST2 via Conda

Now, install BEAST2 using Conda:

conda install -c bioconda beast2
  • Type Y when prompted to proceed with the installation.
  • Conda will resolve dependencies and install BEAST2 along with the appropriate Java version.

9. Verify the Installation

beast -help

You should see usage information for BEAST2.

10. Ensure treeannotator Is Available

which treeannotator

If the path to treeannotator is displayed, it means the command is available.

Test Run

11. Run treeannotator

Now you can run treeannotator using the alias or the command.

Example Command:

Assuming that the fmd-viet-treelog.trees file are

treeannotator -burnin 10 -heights median fmd-viet-treelog.trees atlas_test.tre

Ensure that you are in the directory containing your input file fmd-viet-treelog.trees or provide the full path to the file.

End Session

12. Deactivate the Conda Environment When Done

After you’re finished, you can deactivate the environment:

conda deactivate