From 3eb4a05f8503660ae59ae48d4e75f673bb948b72 Mon Sep 17 00:00:00 2001 From: richelbilderbeek Date: Wed, 18 Dec 2024 10:10:59 +0100 Subject: [PATCH] Fix markdown --- docs/cluster_guides/cluster_speeds.md | 1 - docs/hardware/clusters/bianca.md | 26 ++++++++-------- docs/workshops_courses/awk.md | 44 ++++++++++++++++----------- 3 files changed, 40 insertions(+), 31 deletions(-) diff --git a/docs/cluster_guides/cluster_speeds.md b/docs/cluster_guides/cluster_speeds.md index 8deee9a65..93dbfd572 100644 --- a/docs/cluster_guides/cluster_speeds.md +++ b/docs/cluster_guides/cluster_speeds.md @@ -89,4 +89,3 @@ Project |Setting |Real loading time -----------|----------------------------|----------------- Bianca |Website |2m3.184s - diff --git a/docs/hardware/clusters/bianca.md b/docs/hardware/clusters/bianca.md index d62b8a575..b83db40b7 100644 --- a/docs/hardware/clusters/bianca.md +++ b/docs/hardware/clusters/bianca.md @@ -21,20 +21,20 @@ tags: ## Parameters -Parameter |Bianca +Parameter |Bianca ------------------------|----------------------------------- -**Purpose** |Sensitive data -**Reserved for** |NAISS-SENS projects -**Nodes (Intel)** |272 + 4 nodes á 2 NVIDIA A100 GPUs -**Cores per node** |16/64 -**Memory per node** |128GB -**Fat nodes** |256 & 512GB -**Local disk (scratch)**|4TB -**Network** |Dual 10Gbit/s -**Operating System** |CentOS 7 -**Login nodes** |Yes (2 cores and 15 GB) -**"Home" storage** |Castor -**"Project" Storage** |Castor +**Purpose** |Sensitive data +**Reserved for** |NAISS-SENS projects +**Nodes (Intel)** |272 + 4 nodes á 2 NVIDIA A100 GPUs +**Cores per node** |16/64 +**Memory per node** |128GB +**Fat nodes** |256 & 512GB +**Local disk (scratch)**|4TB +**Network** |Dual 10Gbit/s +**Operating System** |CentOS 7 +**Login nodes** |Yes (2 cores and 15 GB) +**"Home" storage** |Castor +**"Project" Storage** |Castor ## CPU diff --git a/docs/workshops_courses/awk.md b/docs/workshops_courses/awk.md index a7d81616f..0775689e0 100644 --- a/docs/workshops_courses/awk.md +++ b/docs/workshops_courses/awk.md @@ -1,4 +1,5 @@ # 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. @@ -10,6 +11,7 @@ This two-days workshop aims to promote and demonstrate the flexibility of the to - 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. @@ -22,43 +24,50 @@ Use what you learn and dive into the basic concepts of bioinformatics with simpl ## Schedule + --- + ### 1-st day 9:15 - 12:00 + [Seminar session](https://pmitev.github.io/to-awk-or-not/) - - 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](https://pmitev.github.io/to-awk-or-not/Exercises/Exercises/) 13:15 -16:00 - - Solving interactively the exercise problems +- 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](https://pmitev.github.io/to-awk-or-not/Case_studies/manipulating_vcf/) - - Filtering and formatting raw data - - Counting and piling features - - Indexing and hashing to compare variants and annotations + +- Awk for bioinformaticians - seminar +- Case Study: [Manipulating the output from a genome analysis - vcf and gff](https://pmitev.github.io/to-awk-or-not/Case_studies/manipulating_vcf/) +- 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](https://pmitev.github.io/to-awk-or-not/More_awk/Command_params/) - - Declaring and calling functions in awk - [link](https://pmitev.github.io/to-awk-or-not/More_awk/User_defined_functions/) - - 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](https://pmitev.github.io/to-awk-or-not/More_awk/Input_output/) - - Handy tips: awk oneliners use with Vim, gnuplot… +- 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](https://pmitev.github.io/to-awk-or-not/More_awk/Command_params/) +- Declaring and calling functions in awk - [link](https://pmitev.github.io/to-awk-or-not/More_awk/User_defined_functions/) +- 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](https://pmitev.github.io/to-awk-or-not/More_awk/Input_output/) +- Handy tips: awk oneliners use with Vim, gnuplot… Also: [Suggest topic](https://forms.gle/usYYkbWaZVkNceSK6) for discussion or see recently [suggested topics](https://docs.google.com/forms/d/1tQYWc504BQ-uYRA7MWgu1pNXM613r4Ua1wP_yBPlNDM/viewanalytics). ## 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 + ^_ @@ -102,7 +111,8 @@ Just follow some tutorial on how to setup and use the virtual Linux environment. - [2015.10](https://docs.google.com/forms/d/1KSab3x3IlXdgtTScXPfHbFR81FrEpZ8j__hOgV8P5wU/viewanalytics) -## Contacts for the course: +## Contacts for the course + --- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425) [Jonas Söderberg](https://katalog.uu.se/empinfo/?id=N2-1277)