diff --git a/docs/workshops_courses/awk.md b/docs/workshops_courses/awk.md index d28c6bd86..9e957b5b3 100644 --- a/docs/workshops_courses/awk.md +++ b/docs/workshops_courses/awk.md @@ -23,29 +23,32 @@ Application: form. ## Schedule -1-st day 9:15 - 12:00 +### 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 + - 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 + - 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… + - 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 @@ -53,7 +56,7 @@ Also: Suggest topic for discussion or see recently suggested topics. ### 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 + ^ +Tilda `~` sign on Mac with Swedish keyboard layout - Alt + ^ ### Linux @@ -62,7 +65,9 @@ Several distributions have other awk flavors installed by default. The easiest f ### 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. @@ -73,30 +78,29 @@ 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}' +- 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 +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 +Pavlin Mitev +Jonas Söderberg +Lars Eklund +Richel Bilderbeek +UPPMAX