Reproducible code using Git and Conda (by GBCS)

In this training we want to give the participants workable knowledge on Git and Conda. With the help of these tools we will show how reproducibility and portability can be achieved for typical compute intensive projects.

Costs: Free!

Material

Is on the GB Services website.

Instructors

From GBCS:
Markus Fritz, Jelle Scholtalbers and Charles Girardot

When & Where

Friday 27th of October
9h-12h in room v207
13h-17h in room 417

Targeted Audience

Anyone writing small scripts to advanced pipelines but with only basic or no knowledge of Git or how to install tools in isolated environments. A basic knowledge of UNIX is expected i.e. participants should be comfortable with executing command line instructions and have a basic understanding of environment variables.

What you will learn

1. to version your work using git
2. how to use git.embl.de to share your work
3. to control the version and the dependencies of tools by using for example modules
4. to install tools in dedicated environments with Conda and maintain several versions of the same tool

Prerequisite

A laptop running Mac or Linux with a terminal to access EMBL servers (spinoza) through ssh.
Alternatively, a windows machine with putty or alike installed (make sure it works!).

Bookings