Environment

As mentioned previously, we will create our conda environment now and add in our modules as we need them.

Installing Conda

I recommend you install Miniconda which is a minimal installer conda. It has a very small footprint and works great.

See the installation instructions here.

Follow the above instructions and check if everything works:

conda --version

This should give you a version number of your installation.

Create Conda Environment

Now we are ready to create our conda environment for our analysis.

Make sure you only use this environment for a single analysis. Do no reuse environments between analyses since this may lead to possible versioning issues and your analysis may not be reproducible when you come back to it several months later!

conda create -n my_cropseq python=3.8

Here we are creating an environment called my_cropseq and stating that the python version is 3.8.

You can use alternative python versioning if you want the latest and greatest features, but I found this version plays best with older modules.

Moving into and out of the environment

We can now step into our environment as follows:

conda activate my_cropseq

And we can step out as follows:

conda deactivate