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Lecturer(s)
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Course content
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Content of lectures: Content of lectures and exercises: 1) Introduction to shell and command line (basic commands, navigating file system) 2) Variables, shell customization 3) Files, directories, links, and permissions 4) String editing, text editors, input, and output 5) Loops and conditional statements 6) Functions 7) Regular expression 8) Using gawk 9) Pipelines and simple scripts 10) Debugging, error management 11) Git and GitHub 12-13) Introduction to cluster computing (Metacentrum) Content of tutorials: As listed above.
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Learning activities and teaching methods
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Group work
- Preparation for classes
- 44 hours per semester
- Class attendance
- 26 hours per semester
- Preparation for exam
- 20 hours per semester
- Preparation for credit
- 10 hours per semester
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Learning outcomes
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The BASH Programming course is designed to equip students with essential skills for working in a command-line environment and creating their BASH scripts. Throughout this course, students will engage in hands-on sessions to practice and deepen their understanding of individual concepts. By the end of this course, students will be able to work with various command-line-based bioinformatical tools and create short pipelines to process their data.
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Prerequisites
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Practical Computing for Biologists
KMB/925
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Assessment methods and criteria
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Test
Credit: practical test (min. 50%)
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Recommended literature
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BLUM R: Linux Command Line and Shell Scripting Bible. Wiley 2008..
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BURTCH KO: Linux Shell Scripting with Bash. Sams Publishing 2004..
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SOBELL MG: Practical Guide to Linux Commands, Editors, and Shell Programming. Prentice Hall 2009..
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