Conda environments

Updated

If software is available through conda, you can install it yourself into your own anaconda environment.

Information on how to create and manage conda environments can be found at this link:
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

  1. Load anaconda3 software module
    module load anaconda3
  2. From there, you will want to create your own local environment
    conda create --prefix ~/my_env
    Where '~/my_env' is a location in storage or in your home directory where you have permission to read and write files.
  3. Activate the new environment
    source activate ~/my_env
  4. Install software using conda. E.g. install "bamm":
    #load the anaconda3 module
    module load anaconda3

    conda create --prefix ~/my_env
    source activate ~/my_env

    # information on conda package found here: https://anaconda.org/bioconda/bamm
    conda install -c bioconda bamm

    And then whenever you wanted to run bamm, you would just have to make sure that you've loaded your conda environment by typing:
    module load anaconda3
    source activate ~/my_env

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