Create awk.md

docs/workshops_courses/awk.md

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+# Awk workshop
+AWK is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool.
+
+This two-days workshop aims to promote and demonstrate the flexibility of the tool, where the overhead of more sophisticated approaches and programming languages is not worth the bother.
+
+Learn how to
+
+- use Awk as an advanced grep command, capable of arithmetic selection rules with control over the content of the matched lines
+- perform simple conversions, analysis or filter you data on the fly making it easy to plot or read in your favorite research tool
+- handle and take advantage on data split over multiple file data sets.
+- use Awk as simple function or data generator
+- perform simple sanity checks on your results
+- Awk for bioinformaticians
+
+Use what you learn and dive into the basic concepts of bioinformatics with simple exercises on typical scientific problems and tasks.
+
+## Venue and registration:
+
+Date: 16 and 17 January, 2025
+Time: 9:15 - 12:00 and 13:15 -16:00
+Location: Zoom: link wil be sent to applicants
+Application: form.
+
+## Schedule
+
+1-st day 9:15 - 12:00
+Seminar session
+Examples of typical problems suitable for Awk “treatment”
+Introduction to the basics of Awk scripting language
+Solving interactively simple problems
+Lunch break
+Exercises 13:15 -16:00
+Solving interactively the exercise problems
+2-nd day 9:15 - 12:00
+Awk for bioinformaticians - seminar
+Case Study: Manipulating the output from a genome analysis - vcf and gff
+Filtering and formatting raw data
+Counting and piling features
+Indexing and hashing to compare variants and annotations
+Lunch break
+Walk-through session on various topics:
+Awk parsing “simultaneously” multiple input files
+Multiple input files - second approach scenario will be discussed.
+How to trick awk to accept options on the command line like regular program i.e. $ script.awk filename parameter1 parameter2 link
+Declaring and calling functions in awk - link
+Input/output to/from an external programs
+Learn how to send input to an external program (might be based on your data) and read the result back - link
+Handy tips: awk oneliners use with Vim, gnuplot…
+Also: Suggest topic for discussion or see recently suggested topics.
+
+## Prerequisites
+
+### MacOS
+The system provided awk version will work for most of the examples during the workshop with few exceptions, which are noted in the online material.
+
+Tilda ~ sign on Mac with Swedish keyboard layout - Alt + ^
+
+### Linux
+
+Several distributions have other awk flavors installed by default. The easiest fix is to install the gnu version gawk i.e. for Ubuntu: sudo apt install gawk
+
+### Windows 10
+
+Ubuntu for Windows 10 - it is better to read from the source, despite it might not be the easiest tutorial. To my experience, this is the best Linux environment without virtualization.
+MobaXterm use the internal package manager to install gawk. The default is provided by Busybox and is not enough for the purpose of the workshop.
+Linux computer center
+Just login to your account and use the provided awk - any version newer than 4 will work.
+rackham3:[~] awk -V GNU Awk 4.0.2 Copyright (C) 1989, 1991-2012 Free Software Foundation.
+
+### Virtual Linux Machine
+
+Just follow some tutorial on how to setup and use the virtual Linux environment.
+
+### VirtualBox
+
+Ubuntu on Public Clouds
+GitHub & Binder (you need only a browser)
+Singularity
+singularity run shub://pmitev/Teoroo-singularity:gawk 'BEGIN{ for(i=1;i<=4;i++) print i}'
+
+## Feedback from previous workshops:
+
+2024.08 | 2024.01
+2023.09 | 2023.01*
+2022.09 | 2022.01
+​2021.09 | 2021.01
+2020.08 | 2020.01
+2019.08 | 2019.01
+2018.08 | 2018.01
+2017.01 | 2017.08
+2016.08 | 2016.01
+2015.10
+* not enough data to be anonymous
+
+## Contacts for the course:
+
+Pavlin Mitev
+Jonas Söderberg
+Lars Eklund
+Richel Bilderbeek
+UPPMAX
+