Conda environment from our environment.yml
You have Miniconda or Anaconda installed.
Open your terminal shell (e.g. Bash or Zsh).
source ~/miniconda3/bin/activate. If neither works, please first follow Setting path to Conda from your terminal shell. You probably need to restart your shell terminal. Then try to activate
Run the following command:
$ conda env create -f https://raw.githubusercontent.com/coderefinery/software/main/environment.yml
Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:
$ conda env list
In the workshop, we will ask you to activate this environment.
First, follow the steps 1 and 2 in the above section (i.e. open your terminal shell and activate
Then run the following:
$ conda activate coderefinery
Alternatively you can use:
$ source activate coderefinery
Please note however that
conda activate is preferred command since Conda v4.4.
If this does not work, the
coderefinery part should be replaced with the whole path, for example:
$ source activate ~/Miniconda3/envs/coderefinery
How to verify the environment
Once activated, try the following 5 commands. You should see versions printed and not see errors (exact version numbers are not too important):
$ python --version Python 3.11.0
$ jupyter-lab --version 3.6.3
$ pytest --version 7.4.0
$ sphinx-build --version sphinx-build 5.3.0
$ snakemake --version 7.22.0
$ conda deactivate
If you don’t need the
coderefinery environment anymore, it is best to delete
it. The following command will delete the whole environment:
$ conda remove --name coderefinery --all
In case you have both Anaconda3 and Miniconda3, check from which base
coderefinery environment was created, and first activate the
corresponding base environment for the above command to work.
If you have an old
coderefinery environment from a previous workshop
In this case it is safest to delete the old environment and recreate it.