Optionally, you may specify a version of python and add packages at the same time. This creates an environment named my_env. The minimal command to create and environment is : conda create -name my_env This list can always be re-ordered and/or added to later if you desire. I suggest this order because as you add each channel, it moves to the top of a priority list. Īdd channels from which to install packages in the following order: conda config -add channels defaults Follow the installation instructions under the heading “Regular Installation” at. You will never need most of the packages in Anaconda, and with the conda included with Miniconda3 you can install any version of python and any python packages you need to support your bioinformatic programs. To get conda, I suggest that you install Miniconda3. Then you can create multiple environments, each containing compatible programs and dependencies, and switch between the environments as you need to. previously compiled) versions of programs and their dependencies that do not conflict with one another. With conda you create virtual environments into which you install binary (i.e. The second problem usually results from the programs having dependencies that conflict with one another. The first problem may be because installation depends on a specific compiler version you do not have, it has dependencies you do not have installed, or it requires versions of dependencies differing from what you have installed. You may have already found that you could not install a particular program, or that adding another program broke one or more previously installed programs. All three of these python distributions include conda, a package and virtual environment manager. Conda installs programs from repositories called channels, and Bioconda is a channel devoted to bioinformatic programs.Ĭonda allows you to solve problems often encountered when installing bioinformatics programs.

The minicondas (you probably guessed it) are smaller and do not take up as much drive space because they do not include all of the packages found in Anaconda. Miniconda comes in two versions: Miniconda2 is a python 2.7 distribution while Miniconda3 is a python 3 distribution.

Anaconda, Miniconda, Conda, Bioconda – what’s with all of these condas? Anaconda is a full blown python distribution including over 720 open source packages.

Conda env list