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) $
Environment variables
To list any variables you may have, run conda env config vars list.
To set environment variables, run conda env config vars set my_var=value.
Once you have set an environment variable, you have to reactivate your environment: conda activate test-env.
To check if the environment variable has been set, run echo $my_var or conda env config vars list.
When you deactivate your environment, you can use those same commands to see that the environment variable goes away.
You can specify the environment you want to affect using the -n and -p flags. The -n flag allows you to name the environment and -p allows you to specify the path to the environment.
To unset the environment variable, run conda env config vars unset my_var -n test-env.
Environment variables set using conda env config vars will be retained in the output of conda env export. Further, you can declare environment variables in the environment.yml file as shown here:
name: env-name
channels:
- conda-forge
- defaults
dependencies:
- python=3.7
- codecov
variables:
VAR1: valueA
VAR2: valueB
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) ... $.
