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:

conda 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:

conda 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:

conda info --envs # you can also use "conda env list" command

The active environment will be marked with an asterisk.

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

conda list

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

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

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

• Now, deactivate the environment by running conda 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 (SRA-Tools) to our environment using conda install. Make sure that project_a is the active environment first.

conda install -c bioconda sra-tools

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

conda search -c bioconda sra-tools

• Now try to install a different version of SRA-Tools, e.g.:

conda install -c bioconda sra-tools=2.7.0

Read the information that Conda displays in the terminal. It probably asks if you want to downgrade the initial SRA-Tools installation to the one specified here (2.7.0 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 Bowtie2 software to align your reads.

• Find out what versions of Bowtie2 are available in the Bioconda channel using conda search -c bioconda.
• Now install the latest available version of Bowtie2 in your project_a environment.

Let's further assume that you have an old project (called Project Old) where you know you used Bowtie2 2.2.5. 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 Bowtie 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 Bowtie2 without interfering with your new Project A where you want the latest version.

• Make a new environment for your old project:

conda create -n project_old -c bioconda bowtie2=2.2.5

• List your environments (do you remember the command?).
• Activate project_old and check the Bowtie2 version (bowtie2 --version).
• Activate project_a again and check the Bowtie2 version.

Removing packages#

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

conda remove sra-tools

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

conda 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:

conda 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.