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Example: Create and Use Biopython Environment with Conda

Using conda to create an environment that uses the biopython package

To use Conda you must first load the anaconda module:

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module load conda

Create an empty conda environment to install biopython:

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conda-env-mod create -n biopython

Now activate the biopython environment:

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module load use.own
module load conda-env/biopython-py3.12.5

Install the biopython packages in your environment:

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conda install --channel anaconda biopython -y
Fetching package metadata ..........
Solving package specifications .........
.......
Linking packages ...
[    COMPLETE    ]|################################################################

The --channel option specifies that it searches the anaconda channel for the biopython package. The -y argument is optional and allows you to skip the installation prompt. A list of packages will be displayed as they are installed.

Remember to add the following lines to your job submission script to use the custom environment in your jobs:

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module load conda
module load use.own
module load conda-env/biopython-py3.12.5

If you need further help or run into any issues with creating environments, contact us or drop by a coffee hour session for in-person help.

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