UNIX Shell Scripting in Life Sciences
Start: Tuesday, 13 June 2023 @ 00:00
End: Thursday, 15 June 2023 @ 00:00
Scripting allows shell users to automate repetitive tasks, thus improving reproducibility, reducing the risk of errors, freeing time, and avoiding boredom.
Bioinformatics analysis pipelines may involve dozens or hundreds of steps that are each carried out by different command-line programs: assembling these into scripts allows users to treat whole pipelines as if they were ordinary shell commands.
This course targets users who have basic knowledge of interactive shell use (such as taught in the SIB's First Steps with UNIX for Life Scientist and are interested in moving from interactive to automated tasks.
At the end of the course, the participants should understand:
* the main syntactic constructs of Bash (tests, conditionals, loops, functions)
* how to read input and write output
* how Bash stores and processes data (including the various kinds of expansion)
* how to pass and parse command-line arguments and options, as well
* how to to assemble individual analysis steps into reproducible, automated pipelines
Knowledge / competencies
This course is designed for intermediate level users. They are expected to know how to use a Unix shell interactively, i.e., moving around the filesystem, understanding pathnames, lauching programs that work on data, redirecting output to files or other programs, etc.
They are also expected to have some familiarity with basic shell utilities like grep, cut, tr, etc (although no expert skills are required).
Notions of programming (in any language) will be useful, but not essential.
Finally, some proficiency with a text editor is a must.
More details here
A laptop with a command line terminal and a recent version of Bash (4.0 or newer should be ok) installed. The alternative for Windows users is to activate WSL/WSL2.
Registrations for this course are open.
Registration fees for academics are 180 CHF and 900 CHF for for-profit companies.
Deadline for registration and free-of-charge cancellation is set to 31/05/2023. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.
You will be informed by email of your registration confirmation.
Venue and Time
The course will take place at the University of Bern, classroom information will be sent to the participants. It will start at 9:00 CET and end around 17:00 CET. The participants will get detailed information before the course.
Helper: Robin Engler
Coordination: Grégoire Rossier
We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).
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Organizer: SIB Swiss Institute of Bioinformatics