Let’s assume that you are just about to start a new exciting research project called Project A.

Creating Conda environments

• Let’s make our first Conda environment:

mamba create -n project_a -c bioconda fastqc

This will create an environment called project_a, containing FastQC from the Bioconda channel. Conda will list the packages that will be installed and ask for your confirmation.

• Once it is done, you can activate the environment:

mamba activate project_a

By default, Conda will add information to your prompt telling you which environment that is active.

• To see all your environments you can run:

mamba info --envs

The active environment will be marked with an asterisk.

• To see the installed packages and their versions in the active environment, run:

mamba list

• To save the installed packages to a file, run:

mamba env export --from-history > environment.yml

Where --from-history only reports the packages requested to be installed and not additional dependencies. A caveat is that if no version was originally specified, then it is not included in the export file either.

• Now, deactivate the environment by running mamba deactivate.
• List all environments again. Which environment is now marked as active?
• Try to run FastQC:

fastqc --version

• Did it work? Activate your project_a environment and run the fastqc --version command again. Does it work now?

Hopefully the FastQC software was not found in your base environment (unless you had installed it previously), but worked once your environment was activated.

Adding more packages

• Now, let’s add another package (MultiQC) to our environment using conda install. Make sure that project_a is the active environment first.

mamba install -c bioconda multiqc

• If we don’t specify the package version, the latest available version will be installed. What version of MultiQC got installed?
• Run the following to see what versions are available:

mamba search -c bioconda multiqc

• Now try to install a different version of MultiQC, e.g.:

mamba install -c bioconda multiqc=1.13

Read the information that Conda displays in the terminal. It probably asks if you want to downgrade the initial MultiQC installation to the one specified here (1.13 in the example). You can only have one version of a given package in a given environment.

Let’s assume that you will have sequencing data in your Project A, and want to use the latest BBMap software to align your reads.

• Find out what versions of BBMap are available in the Bioconda channel using mamba search -c bioconda bbmap.
• Now install the latest available version of BBMap in your project_a environment.

Let’s further assume that you have an old project (called Project Old) where you know you used BBMap 37.10. You just got back reviewer comments and they want you to include some alignment statistics. Unfortunately, you haven’t saved that information so you will have to rerun the alignment. Now, it is essential that you use the same version of BBMap that your results are based on, otherwise the alignment statistics will be misleading. Using Conda environments this becomes simple. You can just have a separate environment for your old project where you have an old version of BBMap without interfering with your new Project A where you want the latest version.

• Make a new environment for your old project:

mamba create -n project_old -c bioconda bbmap=37.10

• List your environments (do you remember the command?).
• Activate project_old and check the BBMap version (bbmap.sh --version).
• Activate project_a again and check the BBMap version.

Removing packages

Now let’s try to remove an installed package from the active environment:

mamba remove multiqc

• Run mamba deactivate to exit your active environment.
• Now, let’s remove an environment:

mamba env remove -n project_old

After making a few different environments and installing a bunch of packages, Conda can take up some disk space. You can remove unnecessary files with the command:

mamba clean -a

This will remove package tar-balls that are left from package installations, unused packages (i.e. those not present in any environments), and cached data.

Quick recap
In this section we’ve learned:

• How to use mamba install for installing packages on the fly.
• How to create, activate and change between environments.
• How to remove packages or environments and clean up.