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DTSTART:20240522T090000Z
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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/20240116_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 be able to:\n\n* Explain 
 how Bash processes input\, distinguishing in particular between the differ
 ent types of expansion and their purposes\n* Differentiate between the var
 ious syntactic constructs of Bash\, identifying their purposes and how the
 y are used\n* Integrate knowledge of tests\, conditionals\, loops\, functi
 ons\, as well as the various forms of expansion  and other features of Bas
 h to create a script that solves a given problem. \n\n\n\n# Prerequisites\
 n**Knowledge / competencies**\n\nThis course is designed for intermediate 
 level users. They are expected to know how to use a Unix shell interactive
 ly\, i.e.\, moving around the filesystem\, understanding pathnames\, lauch
 ing programs that work on data\, redirecting output to files or other prog
 rams\, etc.\nThey are also expected to have some familiarity with basic sh
 ell utilities like grep\, cut\, tr\, etc (although no expert skills are re
 quired).\nNotions of programming (in any language) will be useful\, but no
 t essential.\nFinally\, some proficiency with a text editor is a must.\n\n
 More details [here](https://sibcloud-my.sharepoint.com/:b:/r/personal/patr
 icia_palagi_sib_swiss/Documents/TrainingGroup-Shared/Courses/2024/20240522
 _ADVUN/prerequisites.pdf?csf=1&amp\;web=1&amp\;e=BFfujJ)\n\n\n\n\n**Techni
 cal**\n\nA laptop with a command line terminal and a recent version of Bas
 h (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/a
 bout).\n\n# Application\n\nRegistration fees for academics are **200 CHF**
  and **1000 CHF** for for-profit companies. \n\nWhile participants are reg
 istered on a first come\, first serve basis\, exceptions may be made to en
 sure diversity and equity\, which may increase the time before your regist
 ration is confirmed.\n\nApplications will close as soon as the places will
  be filled up\, until **07/05/2024**. Deadline for free-of-charge cancella
 tion is set to **08/05/2024**. Cancellation after this date will not be re
 imbursed.\n\nYou will be informed by email of your registration confirmati
 on. Upon reception of the confirmation email\, participants will be asked 
 to confirm attendance by paying the fees within 5 days.\n\n\n# Venue and T
 ime\nThis course will only be streamed.\n\nIt will start at 9:00 CEST and 
 end around 17:00 CEST. \n\nPrecise information will be provided to the par
 ticipants before the course.\n\n\n\n\n\n#  Additional information\n\n\n**C
 oordination:** Diana Marek\, SIB Training group\n\nWe will recommend 0.5 E
 CTS 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 inf
 ormed of all future courses and workshops\, as well as all important deadl
 ines using the form [here](https://lists.sib.swiss/mailman/listinfo/course
 s).\n\nPlease note that participation in SIB courses is subject to our [ge
 neral conditions](https://www.sib.swiss/training/terms-and-conditions).\n\
 nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/even
 ts/code-of-conduct). Participants of SIB courses are also required to abid
 e 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/20240522_ADVUN
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