The problem and its solution

A typical bioinformatics workflow involves dozens of different tools, sometimes each requiring a broad range of libraries and other dependencies. Installing all of them is a tedious task sometimes, an impossible task when different packages require different versions of the same tool.

There are two main solutions to the problem: one is to rely on containers (which resolve the problem of conflicting packages, but does not necessarily simplify the installation of the packages) or package managers.

Miniconda: a popular solution

Miniconda is a package manager that was developed to simplify the installation of Python tools and the creation of isolated environments (to allow, for example, the insulation of conflicting packages).

Miniconda quickly became a fantastic solution to the problem providing:

• a package manager that runs in the user space (not requiring sudo privilege)
• an easy way to add new packages to the repository (in fact, repositories)

Installing conda

The latest version is available from the offical website. There are installer for Linux, macOS and Linux, and based on different versions of Python: copy the link for your platform and the version desired (avoid Python 2.7 and 32-bit versions):

Here a typical workflow (changing the URL accordingly), that will install Miniconda in your home directory (~/miniconda3).

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wget -O install.sh "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
bash install.sh

This will start an interactive process that will ask some questions (to accept the license and to start the initializer).

When the process is finished you’ll be asked to restart your shell (i. e. to log out and login again, or simply try typing source ~/.bashrc on most systems)

Repositories

Conda allows to install packages from a default channel (mainly containing python modules), but also supports third party channels. There are three channels that can be of particular interest in (bio)data science:

• bioconda contains bioinformatics programs (and bioinformatics R libraries)
• conda-forge contains updated versions of commonly used command-line utilities
• r specializes on R libraries

For example, to check if samtools is available in bioonda, and which versions:

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conda search -c bioconda samtools

To install it you can either accept the last compatible version:

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conda search -c bioconda samtools

or specify the version you require:

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conda search -c bioconda samtools=1.10

To install a package, simply replace search with install. If you also add -y you will not be prompted and will try to install directly.

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conda install -y -c bioconda vsearch

We can add some channels to a configuration file so that conda always checks them when searching. This will make some searches slower so I generally only add conda-forge, but adding also bioconda can be appropriate. Avoid adding r: it’s massive and rarely used in bioinformatics (most biological R packages are available in bioconda).

To add some channels in your configuration file, create (or edit) the ~/.condarc file as follows:

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channels:
  - defaults
  - conda-forge
  - bioconda

Creating and using environments

Conda simplifies installing package, but a problem remains: conflicting versions. You may want to use samtools 1.10, for example, but another tool installed an older version because it’s not yet ready to support a more recent one.

Conda allows to create environments, that are isolated rooms where you can install packages independently from other rooms.

Create a new environment

We need to choose a unique name for our new environment, in this example myenv1 (usually it’s the name of a tool (like qiime2-2020.1) or a task (like denovo):

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conda create -n myenv1

Activate the environment

To use an environment we need first to activate it:

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conda activate myenv1

When the environment is active, you will no longer be able to access the packages you installed in the base environment, and if you install a package now it will belong to the active environment.

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conda install -c bioconda vsearch=2.17

Deactivate the environment

To return to the previous environment:

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conda deactivate

List your environments

To get a list of the environments in your system:

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conda info --envs

Delete an environment

To be used with care:

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conda remove -n ENVIRONMENT_NAME --all

Using mamba for faster installations

you can now update your conda to become faster as mamba see how.

Sometimes we require a lot of packages to be installed and this will trigger a long process called “solving the environment”. There is a drop-in replacement for Conda called mamba, that you can install from conda-forge:

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conda install -y -c conda-forge mamba

Then just replace “conda” with “mamba” to use it, for example:

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mamba search -c bioconda seqfu

and to install (for example):

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mamba install -c bioconda seqfu

See also:

• Introdution to conda by Astrobiomike
• Install Miniconda (video)