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DESCRIPTION:# Overview\nScripting allows shell users to automate repetitive
  tasks\, thus improving reproducibility\, reducing the risk of errors\, fr
 eeing time\, and avoiding boredom.\n\nBioinformatics analysis pipelines ma
 y involve dozens or hundreds of steps that are each carried out by differe
 nt command-line programs: assembling these into scripts allows users to tr
 eat whole pipelines as if they were ordinary shell commands.\n\n# Audience
 \nThis course targets users who have basic knowledge of interactive shell 
 use (such as taught in the SIB's [First Steps with UNIX in Life Sciences](
 https://www.sib.swiss/training/course/20230110_FSWU)) and are interested i
 n moving from interactive to automated tasks.\n\n# Learning objectives\nAt
  the end of the course\, the participants should understand:\n* the main s
 yntactic constructs of Bash (tests\, conditionals\, loops\, functions)\n* 
 how to read input and write output\n* how Bash stores and processes data (
 including the various kinds of expansion)\n* how to pass and parse command
 -line arguments and options\, as well\n* how to to assemble individual ana
 lysis steps into reproducible\, automated pipelines\n\n# Prerequisites\n**
 Knowledge / competencies**\n\nThis course is designed for intermediate lev
 el 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 program
 s\, etc.\nThey are also expected to have some familiarity with basic shell
  utilities like grep\, cut\, tr\, etc (although no expert skills are requi
 red).\nNotions of programming (in any language) will be useful\, but not e
 ssential.\nFinally\, some proficiency with a text editor is a must.\n\nMor
 e details [here](https://sibcloud-my.sharepoint.com/:b:/g/personal/patrici
 a_palagi_sib_swiss/EUg9dFU1_uBGm846H1n53J0BOg7jzkA1fDYQh3lCcr3_lA?e=WgrKKn
 )\n\n\n\n**Technical**\n\nA laptop with a command line terminal and a rece
 nt version of Bash (4.0 or newer should be ok) installed. The alternative 
 for Windows users is to activate [WSL/WSL2](https://learn.microsoft.com/en
 -us/windows/wsl/about).\n\n# Application\nRegistrations for this course ar
 e open.\n\nRegistration fees for academics are **300 CHF** and **1500 CHF*
 * for for-profit companies. \n\nDeadline for registration and free-of-char
 ge cancellation is set to *31/05/2023*. Cancellation after this date will 
 not be reimbursed. Please note that participation to SIB courses is subjec
 t to our [general conditions](http://www.sib.swiss/training/terms-and-cond
 itions).\n\nYou will be informed by email of your registration confirmatio
 n.\n\n# Venue and Time\nThe course will take place at the University of La
 usanne\, classroom information will be sent to the participants. It will s
 tart at 9:00 CET and end around 17:00 CET. The participants will get detai
 led information before the course.\n\n\n\n\n\n#  Additional information\nH
 elper: Robin Engler \nCoordination: Grégoire Rossier\n\nWe will recommend
  0.75 ECTS credits for this course (given a passed exam at the end of the 
 course).\n\nYou are welcome to register to the SIB courses mailing list to
  be informed of all future courses and workshops\, as well as all importan
 t deadlines using the form [here](https://lists.sib.swiss/mailman/listinfo
 /courses).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-eu
 rope.org/events/code-of-conduct). Participants of SIB courses are also req
 uired to abide by the same code.\n\nFor more information\, please contact 
 [training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:UNIX Shell Scripting in Life Sciences
URL;VALUE=URI:https://www.sib.swiss/training/course/20230613_ADVUN
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