Conda Environment

The following steps allow you to create and use your own virtual environment to run the Processing Chain. We recommend using a conda environment for the usage of the provided scripts. Please follow the instructions for the installation. The following steps only need to be performed once.

1. Install Miniconda

Install Miniconda as user-specific Miniconda, e.g., in your $HOME directory, which is the default location.

Note

Only conda itself should be installed in your $HOME. All environments should be stored in your $PROJECT directory; otherwise, you risk filling up your $HOME directory. See below for instructions.

To install the latest Miniconda, type:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Further details on Miniconda can be found on the Miniconda documentation page.

2. Create the Conda Environment

Create a conda environment proc-chain and install the requirements:

conda env create --prefix $PROJECT/envs/proc-chain -f env/environment.yml

To be able to activate your conda environment by simply using conda activate proc-chain instead of the full path, add the following to your .bashrc:

export CONDA_ENVS_PATH=$PROJECT/envs

Activate the environment (use “source activate” in case “conda activate” does not work):

conda activate proc-chain

If you already have the environment but want to update it:

conda env update --file env/environment.yml --prune

3. Store user-specific data

To register your email address and standard project account, store them in these files within your home directory:

echo <your_account_id> > ~/.acct
echo <your_email_address> > ~/.forward

These settings are optional. The Processing Chain will first check the content of those files. If desired, the corresponding variables can be overridden by setting the compute_account and user_mail variables in the config.yaml file.