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DTSTART:20221107T000000Z
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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 for Life Scientist
 ](https://www.sib.swiss/training/course/20220927_FSWU) and are interested 
 in moving from interactive to automated tasks.\n\n# Learning objectives\nA
 t the end of the course\, the participants should understand:\n* the main 
 syntactic 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 comman
 d-line arguments and options\, as well\n* how to to assemble individual an
 alysis steps into reproducible\, automated pipelines\n\n# Prerequisites\n#
 #### Knowledge / competencies\nThis course is designed for intermediate le
 vel users. They are expected to know how to use a Unix shell interactively
 \, i.e.\, moving around the filesystem\, understanding pathnames\, lauchin
 g programs that work on data\, redirecting output to files or other progra
 ms\, etc.\nThey are also expected to have some familiarity with basic shel
 l utilities like grep\, cut\, tr\, etc (although no expert skills are requ
 ired).\nNotions of programming (in any language) will be useful\, but not 
 essential.\nFinally\, some proficiency with a text editor is a must.\n\nMo
 re details [here](https://sibcloud-my.sharepoint.com/:b:/g/personal/patric
 ia_palagi_sib_swiss/EUg9dFU1_uBGm846H1n53J0BnZCrhaoq-P5ynt0oT5Yu8w?e=gJSVv
 u)\n\n\n\n##### Technical\nA laptop with a command line terminal and a rec
 ent 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/e
 n-us/windows/wsl/about).\n\n# Application\nRegistrations for this course a
 re open.\n\nRegistration fees for academics are **120 CHF** and **600 CHF*
 * for for-profit companies. \n\nDeadline for registration and free-of-char
 ge cancellation is set to *31/10/2022*. 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 Be
 rn\, classroom information will be sent to the participants. It will start
  at 9:15 CET and end around 17:00 CET. The participants will get detailed 
 information before the course.\n\n\n\n\n\n#  Additional information\nHelpe
 r: Robin Engler \nCoordination: Grégoire Rossier\n\nWe will recommend 0.5
  ECTS credits for this course (given a passed exam at the end of the cours
 e).\n\nYou are welcome to register to the SIB courses mailing list to be i
 nformed of all future courses and workshops\, as well as all important dea
 dlines using the form [here](https://lists.sib.swiss/mailman/listinfo/cour
 ses).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.
 org/events/code-of-conduct). Participants of SIB courses are also required
  to abide by the same code.\n\nFor more information\, please contact [trai
 ning@sib.swiss](mailto://training@sib.swiss).
SUMMARY:UNIX Shell Scripting in Life Sciences
URL;VALUE=URI:https://www.sib.swiss/training/course/20221107_ADVU
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