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