First steps with Conda

Configuring Conda and installing mamba.

Pre-requisite #

Activate the base Conda environment, as demonstrated in the page Install Miniconda.

Help and information #

The conda --help command can be used to list the main sub-commands of the conda executable, along with a brief description of their purpose.

conda --help

The conda info command can be used to display information about your current installation.

conda info

Configuration #

Conda packages are stored in different locations called channels. More information is available in the Conda documentation →.

Configured channels are searched in a specific order when installing packages, so it is important to configure which channels are searched and in which order.

We recommend the following channels, in decreasing order of priority:

• bioconda
• conda-forge
• default

In other words, Conda will attempt to install packages from the bioconda channel first, and then sequentially search the channels conda-forge and defaults when packages cannot be found in earlier channels in the priority list.

Adding new channels automatically moves them to the top of the priority list. With that in mind, the commands below sequentially add channels from the lowest priority channel to the highest priority one, to produce the desired order of priority described above.

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

The conda info command (described earier on this page) can be used to verify the list of channels that are currently configured, among other pieces of information.

List installed packages #

The conda list command can be used to list the packages installed in the current environment.

conda list

Update installed packages #

The conda update command can be used to updates conda packages (in the current environment) to the latest compatible version.

The --all option checks all packages in the environment (rather than explicitly specifying individual packages).

conda update --all

In particular, the command will produce a detailed plan, listing packages that may be downloaded and updated in the Conda environment.

We recommend careful reviewing the information detailed in the package update plan before agreeing to proceed, by typing y and pressing the Return key when prompted.

Update Conda itself #

Part of the output of the conda update command may report whether a newer version of the conda package itself is available, alongside instructions to update that package.

Follow those instructions when you are ready to update your Conda installation.

conda update -n base -c defaults conda

Search available packages #

The conda search command can be used to search for packages available in any of the configured channels.

For instance, the example below demonstrates how to search for a Conda package called mamba. Note that the list of results was rather long and only the first results are shown in the screenshot.

conda search mamba

The output of the conda search command includes key information for identifying the list of versions available and potentially selecting a specific build to install. For instance, the Channel column indicates the channel in which each package build is stored, which can be especially important for packages available from different channels.

Verify that a package is not installed #

The conda list <package> command can be used with the name of a specific package, to list any version of that package installed in the environment.

The output will be presented as a table, and the table will be empty (i.e., only column headers) if the package is not currently installed in the environment.

conda list mamba

Alternatively, the Bash command which can be used to check whether an executable known to be present in a Conda package is detected on the PATH.

which mamba

Install a package #

The conda install command can be used to install packages.

However, the built-in Conda installer can be quite slow to identify and resolve dependencies between packages, which led to a re-implementation of the conda package manager in C++, distributed in the mamba package.

Install the mamba package using the command below. Make sure to type y and press the Return key when prompted to proceed with the package plan.

conda install mamba

Verify that a package is installed #

In the example below, the conda list <package> command is used to list installed packages that contain the pattern mamba in their name.

conda list mamba

In the example below, the Bash command which is used to display the location of the executable mamba that is now detected on the PATH.

which mamba

Alternatively, the mamba executable itself can be invoked, for instance with the --help option, to display the help page of the program, implictly verifying that the executable itself is installed and working properly.

mamba --help

Using Mamba #

Mamba is implemented as a drop-in replacement for Conda.

In other words, the mamba executable can be used in many cases as a replacement for the conda executable, to produce the same result much more rapidly.

For instances:

mamba info
mamba update --all
mamba search <package>
mamba install <package>

Replace <package> by the actual name of any package of interest to you.