This is a virtual workshop, you can participate by reading workshop materials, watching video presentations and carrying out exercises on an assigned BioHPC Cloud server (server assignments are listed here). If you need help, please sign up for our Office Hours. The server assigned to you for hands-on exercises will be available for a limited time, see server assignment page or bottom of this page for details. Please note, the server is assigned to you for hands-on exercises, NOT heavy computing, using the server for workshop unrelated computing is not allowed and will result in assignment termination.
We have two goals for participants in this workshop: 1) Learn how to install software on a Linux computer; 2) Understand the basic architecture of Linux software, so you can troubleshoot if a software does not run.
The workshop is composed of two parts:
Part 1. Basic architecture of Linux software and how to install software in Conda. Installing, updating and deleting software in Conda is very easy, and does not require "root" (administrative level) privilege. There are more than 3000 bioinformatics software titles available from Conda.
Part 2. Installation of software without Conda. Most of the commonly used software should be available in the Conda repository. But some software might not be in Conda yet, and some might even require you to compile the source code by yourself. In this session, we will cover software written in PYTHON, C, PERL, R and JAVA.
The workshop is divided into paired sessions: a lecture/presentation session followed by a hands-on session, allowing for plenty of time for hands-on training.
Workshop presentation 1
Workshop presentation 2
Workshop presentation 3
Workshop presentation 4
Workshop server assignment