Andrea Telatin
Andrea Telatin Senior bioinformatician at the Quadram Institute Bioscience, Norwich.

Micromamba package manager

Micromamba package manager

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.

Micromamba: a modern solution

Micromamba 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).

Micromamba 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.

In MacOS you might have “brew” installed, thus you can install micromamba with:



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brew install micromamba

Otherwise, the installation is automated by a script (works for both Linux and MacOs):



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"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

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

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



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micromamba search -c bioconda samtools

:bulb: use the Bioconda website instead to search quickly

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



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micromamba search -c bioconda samtools

or specify the version you require:



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micromamba 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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micromamba 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 ~/.mambarc file as follows:



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channels:
  - conda-forge  
  - bioconda  
channel_alias: https://repo.prefix.dev/

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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micromamba create -n myenv1

You can create a new environment and simultaneously install some packages, for example



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micromamba create -n mapping --yes "samtools>=1.9" minimap2 bwa=0.7
  • the -y or --yes switch will automatically accept the suggested packages and proceed with installation

Activate the environment

To use an environment we need first to activate it:



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micromamba 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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micromamba install -c bioconda vsearch=2.17

:bulb: When running “install” check that you are in the correct environment

Deactivate the environment

To return to the previous environment:



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micromamba deactivate

List your environments

To get a list of the environments in your system:



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micromamba env list

Delete an environment

To be used with care:



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micromamba remove -n ENVIRONMENT_NAME --all

See also: