Conda ​

Conda is a handy environment management system that allows you to reliably install packages and libraries and quickly switch between package versions. We recommend to use faster Micromamba distribution.

Conda in Workbench

This guide is for the installation of Conda on your lab machines when connecting over SSH.

Head over to our Getting started with Conda in Workbench section to learn more about Conda in your Workbench environment.

1. Install Conda ​

1.1 Log into your lab machine and install Miniconda:

bash
echo | "${SHELL}" <(curl -L https://micro.mamba.pm/install.sh);

~/.local/bin/micromamba install -n base -c conda-forge -y "conda" "mamba"

See Installing on Linux for more information on the Micromamba installation.

1.2 After the installation, log out and log into your lab to activate your Conda setup.

bash
exit

Get more out of Conda

To get most out of Conda we recommend reading the guide Conda - Managing environments.

2. Set up Bioconda and Conda-forge channels ​

To find packages in Conda you need to configure relevant channels.

We recommend to start with bioconda and conda-forge channels.

2.1 A quick way to make sure your channels are added correctly is to (re)add them in this order:

bash
conda config --remove channels defaults
conda config --add channels nodefaults
conda config --add channels bioconda
conda config --add channels conda-forge

Read more on how to set up channels in the guide from Bioconda.

3. Install your tools ​

Search for your favorite tool on the Bioconda page and have a field day installing:

bash
# -- Working example
mamba install plink2
# -- or
conda install plink2

TIP

We have a very easy guide on how to get Saige running in Conda.

4. Do cool science ​

Start your favorite tools and do cool science:

bash
plink2 <input>

Additional resources ​

Note that this work with some, but not all, bioconductor-packages. Please send us a note if you need these.

bash
# install
mamba create -n renv -c conda-forge r-base r-essentials
# or
conda create -n renv -c conda-forge r-base r-essentials
conda activate renv

# install package in shell
R CMD INSTALL --library="${CONDA_PREFIX}/lib/R/library" .

# install cran packages within r
install.packages("png", paste(Sys.getenv("CONDA_PREFIX"), "/lib/R/library", sep=""))