Computing Environment Setup for Bioinformatics and Computational Biology

So, you want to harness the immense power of bioinformatics and computational biology for your science?

Here's some advice that will save you headaches and make your life easier when working in a Linux/UNIX environment.

NOTE: These instructions are for setting up your Linux/UNIX computational environment. This might be on your local machine, but it could also be on a computing cluster like TACC that you log into remotely.

Instructions for setting up your local machine (for example, your laptop) are covered over at Computer Setup.

Introduction to the Shell

Login Scripts and your $PATH (.bashrc)

Using TACC

Conda 101

Set up Conda, Mamba, Bioconda

Conda is the main framework. Mamba speeds up Conda installs (once it is installed use mamba everywhere you would use conda for running commands. Bioconda makes it possible to install additional packages related to bioinformatics and computational biology.

1. Install Conda (the Miniconda flavor). Using the Quick Command Line Install instructions is probably easiest, esp. on TACC.
2. Reload your shell (close and open the terminal or logout and log back in) so you are in your conda base environment.
3. Install Mamba using these commands:
   conda install mamba
mamba init
4. Set up Bioconda Run the commands here

Use Environments

Miscellaneous Timesavers

• Setting up SSH Public Key Authentication
  Save yourself typing your password every time you connect to TACC or another server
• Using lftp to copy files to/from UT Box
  Copy and mirror files from/to your computer and TACC or other servers.