Bioinformatics Software Installation with Conda Linux as a Computational Platform: 9/17/2020 Bioinformatics software is all over the place à dependencies complex
• Dependencies are base packages that Python, c, R, rely on. • Can require c programming experience to install, and just not how you want to spend your time. • A version of something required by thing 1 may conflict with a version required by thing 2 • Package managers/installers to the rescue! Conda is for Data Science, Bioinformatics
• Installs python by default- can handle different environments for python 2, 3, and also R. • Anaconda Navigator: GUI • Has jupyterhub • A Script Editor with cool features • Environment and Package Manager • Miniconda: Command Line only • just the environment and package manager • OK to have both • Windows users- Anaconda Navigator and Linux subsystem will be separate environments Installing conda
• Go to: docs.conda.io/en/latest/miniconda.html • Mac OS- 1. right-click on Python 3.8, Miniconda3 Linux 64-bit to copy the link 2. Use wget paste in the link. $ wget
For everyone else: $ conda init
Now moving forward: $ conda config --add channels conda-forge conda-forge is a “channel” where a lot of packages come from. $ conda install numpy $ conda search wget $ conda install tree Let’s install bioinformatics software!!! • $ conda install –c bioconda bwa • bioconda is another channel that has bioinformatics software • Hit