Objectifs :
For your research studies you may need to access a Unix computer and be required to orchestrate computations, to get and summarize information resulting from simulation programs or real data analysis programs. These tasks can be done by manually typing commands in a terminal application on Unix systems. However, once you know the basics of Unix commands, it’s time to think automation: your time is valuable and writing shell scripts to do the repetitive and cumbersome work will help you save some of this precious time.
This three-sessions introduction to shell scripting is aimed at students that already know the basics of commands in a Unix terminal and who want to learn how to automate part of their work by writing shell scripts.
This course emphasizes putting the concepts into practice. After a few slides introducing the ideas and syntax, learners are given numerous practical labs so that they can learn by doing to produce increasingly complex and powerful scripts.
Warning: running scripts as jobs on a computing cluster is out of the scope of this training, this would need a dedicated session. However, the scripts you’ll learn writing during this course might well end up running on a computing cluster, once they ran successfully on your laptop for a dozen times ;-)

Programme :
We will start with the basics: what’s a script and how to run a script. Then, we’ll go over the important headings to begin scripts with.
After writing your first simple scripts running straight commands, we’ll see how a script can be made more flexible with the help of arguments and various variables. This will make your scripts more flexible and usable in different contexts.
Will see how to handle errors met at runtime and how to prevent some errors at the time of the writing.
Wanting to automate a data collection or analysis over the many lines of a result file or over the many files in a folder we will study the various ways to repeat a given process by manufacturing suitable loops. We will also come back on the shell mechanisms allowing to chain commands and see how our loops can be fed with the result of other commands through redirections and pipelines.
Once your knowledge brings you to write scripts whose length exceeds what can be presented on a single screen, it will be time for the next building block: functions. They will allow you to make your shell scripts more readable, reusable and extensible.

Pré-requis :
knowledge of both basic programming and Unix commands is necessary to attend this course. Though, no knowledge on shell scripts is necessary as it will be our central study point during the course.
Note : This course is a follow up of the Learning Unix and its Command Line Interface course, but is opened to other students, provided they have the prementioned prerequisites.

Méthode pédagogique :
presential. Slide presentation + labs on computers. Students are encouraged to come with a laptop hosting a Unix system or with the WSL2 (Ubuntu) app installed in case they have a Windows OS.

Compétences acquises à l'issue de la formation :
Understanding how a script run
Knowing what can be automated on a unix system
Reading and understanding a provided script
Being able to alter a script to complete it with additional tasks or to make it more flexible and reusable.
Being able to write a script from scratch, making it flexible, maintainable and reusable

Les Compétences et capacités visées à l'issue de la formation (fiches RNCP)

Arrêté du 22 février 2019 définissant les compétences des diplômés du doctorat et inscrivant le doctorat au répertoire national de la certification professionnelle. https://www.legifrance.gouv.fr/loda/id/JORFTEXT000038200990/

Bloc 1 : Conception et élaboration d’une démarche de recherche et développement, d’études et prospective

- Identifier et résoudre des problèmes complexes et nouveaux impliquant une pluralité de domaines, en mobilisant les connaissances et les savoir-faire les plus avancés

- S’adapter en permanence aux nécessités de recherche et d’innovation au sein d’un secteur professionnel

Bloc 2 : Mise en œuvre d’une démarche de recherche et développement, d’études et prospective

- Mettre en œuvre les méthodes et les outils de la recherche en lien avec l’innovation

- Garantir la validité des travaux ainsi que leur déontologie et leur confidentialité en mettant en œuvre les dispositifs de contrôle adaptés

Bloc 3 : Valorisation et transfert des résultats d’une démarche R&D, d’études et prospective

- Mettre en œuvre les problématiques de transfert à des fins d’exploitation et valorisation des résultats ou des produits dans des secteurs économiques ou sociaux

- Respecter les principes de déontologie et d’éthique en relation avec l’intégrité des travaux et les impacts potentiels

La formation participe à l'objectif suivant :être directement utile pour la réalisation des travaux personnels de recherche