Easy installations and virtual environments with conda

Maxime Borry

Follow the presentation

What does it mean to install a program ?

-> Copy/move the executable of the program in the PATH

What is the PATH ?

borry@mpi-sdag1:~$ echo $PATH
  • /usr/local/sbin
  • /usr/local/bin
  • /usr/sbin
  • /usr/bin

When can't “install” programms on a computer, it's because you don't have write access to these directories

What's in my path ?

For example, let's have a look at /usr/bin !

borry@mpi-sdag1:~$ ls -1 /usr/bin

Great, but what about Conda ?

I have a confession: this is not my real path

borry@mpi-sdag1:~$ echo $PATH

Here is my real path

borry@mpi-sdag1:~$ echo $PATH

The location where executables will be installed by Conda



“Conda is an open source, cross-platform, language-agnostic package and environment management system distributed by Anaconda.”

  • Free
  • No admin rights required
  • Tons of bioinformatic packages available
  • Easy to install

Install conda

Two distributions:

  • Anaconda (fully featured, heavy)
  • Miniconda (bare minimum)

Installation for Mac

borry@maxime:~$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
borry@maxime:~$ bash ~/miniconda.sh

Installation for Linux

borry@mpi-sdag1:~$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
borry@maxime:~$ bash ~/miniconda.sh

Using conda

Install a package

When you install a package, conda automatically handles the installation of all its dependancies

Jupyter notebook

(base)borry@mpi-sdag1:~$ conda install jupyter

Install a package from a specific channel

(base)borry@mpi-sdag1:~$ conda install -c bioconda bwa

Bioconda: Channel for bioinformatics packages

Bioconda: sustainable and comprehensive software distribution for the life sciences

conda-forge: community-led (huge) collection of recipes

Everything with conda is an environment

An environement is an isolated sandbox that allows a fine control on program's versions and dependancies

By default, you're in the base environment
(base)borry@mpi-sdag1:~$ conda env list
# conda environments:
base          *  /projects1/clusterhomes/borry/miniconda3
But can create new environments…
(base)borry@mpi-sdag1:~$ conda create -n myEnvName

Everything with conda is an environment(2)

Change your current environemnt (activate)
(base)borry@mpi-sdag1:~$ conda activate myEnvName
Note that your prompt now includes the name of the active environment
Install a package in this environment, for example, RStudio
(myEnvName)borry@mpi-sdag1:~$ conda install -c r rstudio
And go back to the base environment
(myEnvName)borry@mpi-sdag1:~$ conda deactivate
The packages installed in one environement are not accessible from outside !

Let's create an environment for MetaPhlan2 and Krona

Krona plots

(base)borry@mpi-sdag1:~$ conda create -n metaphlan
(base)borry@mpi-sdag1:~$ conda activate metaphlan
(metaphlan)borry@mpi-sdag1:~$ conda install -c bioconda metaphlan2
# Now you can use metaphlan !
(metaphlan)conda install -c bioconda krona

Now let's share our environement !

(metaphlan)borry@mpi-sdag1:~$ conda env export > metaphlan_env.yml

And recreate it on another machine from the environment file

(base)borry@maxime:~$ conda env create -f metaphlan_env.yml

Other useful conda commands

List installed packages and versions in an environment
(metaphlan) borry@mpi-sdag1:~$ conda list
Uninstall a package (here Krona)
(metaphlan)borry@mpi-sdag1:~$ conda remove krona
Delete an environment
(base)borry@mpi-sdag1:~$ conda env remove -n metaphlan

Conda documentation: conda.io/docs

Faster conda with Mamba

Mamba is conda drop-in replacement, with a faster dependancy solver.

conda install -c conda-forge mamba

Bonus: building conda recipes