conda.md

layout	title	parent
default	Conda	2. Program guides

Conda

From the website, conda provides "Package, dependency and environment management for any language".

Conda is a package manager allows specific versions of programs to be installed, alongside their dependencies. Different sets of programs can be installed to different virtual environments. A virtual environment is basically a set of programs.

Installing conda

Conda is part of Anaconda, which is available for free. Conda is also available through Miniconda, a free minimal installer for conda.

Conda can be installed on a 64-bit Linux system with the following commands...

# Downloading miniconda
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
# Installing miniconda
$ bash miniconda.sh -b -p $HOME/miniconda
# Updating conda
$ conda update -q conda

Cloning and activating a conda environment

Conda virtual environments can be shared, either as a .yml file or a .txt file. A .yml copy of a conda environment can be used to recreate that environment on another machine, regardless of the operating system platform used. A .txt copy of a conda environment is more explicit: it can be used to create an identical copy of a conda environment using the same operating system platform as the original machine. A conda virtual environment is used throughout this project: a .yml copy and an explicit .txt copy of this conda environment are provided.

A conda environment can be activated using $ conda activate name_of_environment. Once activated, the programs installed in this environment are available. Conda can be deactivated using $ conda deactivate.

The conda environment used throughout this project can be created from bioinfo-notebook.txt and activated using the following commands...

# Creating the bioinfo-notebook environment
/bioinfo-notebook $ conda create --name bioinfo-notebook --file envs/bioinfo-notebook.txt
# Activating the bioinfo-notebook environment
$ conda activate bioinfo-notebook
# Once activated, the environment name is at the start of the bash prompt
(bioinfo-notebook) $

Demonstration

In this video demonstration, a conda virtual environment is created using bioinfo-notebook.txt. This virtual environment is then activated using conda activate bioinfo-notebook. Note that the name of the active conda environment is displayed in brackets at the start of the bash prompt: (name of active environment) ... $.

Further reading

1. Downloading conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html
2. Conda packages: https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/packages.html
3. Conda environments: https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html