update setup, authors, slides

_quarto.yml

@@ -39,9 +39,12 @@ book:
   navbar:
     pinned: true
     logo: "_extensions/cambiotraining/courseformat/img/university_crest_reversed.png"
+    left: 
+      - text: Slides
+        href: https://docs.google.com/presentation/d/1IuEuwLe7TFbn1kYQmHtsRXvFleSVq2wpaYsymMOEatA/edit?usp=sharing
     right:
       - icon: github
-        href: https://github.com/cambiotraining/
+        href: https://github.com/cambiotraining/chipseq
         aria-label: Bioinformatics Training Facility GitHub
       - icon: twitter
         href: https://twitter.com/bioinfocambs

index.md

@@ -59,14 +59,37 @@ The listing below shows an example of how you can give more details about yourse
 These examples include icons with links to GitHub and Orcid. 
 -->
 
-About the authors:
-
+About the authors (alphabetical by surname):
+
+- **Sandra Cortijo**
+  <a href="https://orcid.org/0000-0003-3291-6729" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
+  <a href="https://github.com/scortijo" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
+  _Affiliation_: Centre National de la Recherche Scientifique: Montpellier  
+  _Roles_: writing; conceptualisation; coding
+- **Sergio Martinez Cuesta**
+  <a href="https://orcid.org/0000-0001-9806-2805" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
+  <a href="https://github.com/semacu" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
+  _Affiliation_: AstraZeneca, Cambridge  
+  _Roles_: writing; conceptualisation; coding
+- **Sankari Nagarajan**
+  <a href="https://orcid.org/0000-0001-8748-6223" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
+  _Affiliation_: University of Manchester  
+  _Roles_: writing; conceptualisation
+- **Ashley Sawle**
+  <a href="https://orcid.org/0000-0002-2985-5059" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
+  <a href="https://github.com/AshKernow" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
+  _Affiliation_: Cancer Research UK, Cambridge Institute  
+  _Roles_: writing; conceptualisation; coding  
+- **Denis Seyres**
+  <a href="https://orcid.org/0000-0002-2066-6980" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
+  _Affiliation_: Universitätsspital Basel: Basel  
+  _Roles_: writing; conceptualisation; coding
 - **Hugo Tavares**
   <a href="https://orcid.org/0000-0001-9373-2726" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
   <a href="https://github.com/tavareshugo" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
   _Affiliation_: Bioinformatics Training Facility, University of Cambridge  
-  _Roles_: writing - original draft; conceptualisation; coding
-- **TODO**
+  _Roles_: writing; conceptualisation; coding
+
 
 
 ## Citation
@@ -76,22 +99,21 @@ About the authors:
 Please cite these materials if:
 
 - You adapted or used any of them in your own teaching.
-- These materials were useful for your research work. For example, you can cite us in the methods section of your paper: "We carried our analyses based on the recommendations in _TODO_.".
+- These materials were useful for your research work. For example, you can cite us in the methods section of your paper: "We carried our analyses based on the recommendations in _Cortijo S et al. (2023)_.".
 
 You can cite these materials as:
 
-> TODO
+> Cortijo S, Martinez Cuesta S, Nagarajan S, Sawle A, Seyres D, Tavares H (2023) "cambiotraining/chipseq: Analysis of ChIP-seq Data", https://cambiotraining.github.io/chipseq/
 
 Or in BibTeX format:
 
 ```
 @Misc{,
-  author = {},
-  title = {},
-  month = {},
-  year = {},
-  url = {},
-  doi = {}
+  author = {Cortijo, Sandra AND Martinez Cuesta, Sergio AND Nagarajan, Sankari AND Sawle, Ashley AND Seyres, Denis AND Tavares, Hugo},
+  title = {cambiotraining/chipseq: Analysis of ChIP-seq Data},
+  month = {July},
+  year = {2023},
+  url = {https://cambiotraining.github.io/chipseq/}
 }
 ```
 
@@ -100,4 +122,10 @@ Or in BibTeX format:
 
 <!-- if there are no acknowledgements we can delete this section -->
 
-- TODO
+There are many online resources that inspired our own materials (e.g. package vignettes) and we cite them where relevant. 
+
+We also recommend the following training materials:
+
+- [Understanding chromatin biology using high throughput sequencing](https://hbctraining.github.io/Intro-to-ChIPseq/schedule/2-day.html) from the Harvard Chan Bioinformatics Core
+- [Introduction to ChIPseq using HPC](https://hbctraining.github.io/Intro-to-ChIPseq/schedule/2-day.html) from the Harvard Chan Bioinformatics Core
+- [ChIP-seq analysis](https://www.bioinformatics.babraham.ac.uk/training.html#chip) from the Babraham Institute

setup.md

@@ -23,17 +23,24 @@ The data used in these materials is provided as a zip file.
 Download and unzip the folder to your Desktop to follow along with the materials.
 
 <!-- Note for Training Developers: add the link to 'href' -->
-<a href="">
+<a href="https://www.dropbox.com/sh/0obk40tzxscqdez/AADJVWnZd3h8UoHlbYRq64wVa?dl=1">
   <button class="btn"><i class="fa fa-download"></i> Download</button>
 </a>
 
 ## Setup
 
-If you want to run some of this analysis on your own computer, you can follow these instructions. 
+To run the analysis covered in this workshop, you will broadly need two things: 
+
+- **R/RStudio** for all the downstream analysis (i.e. after peak calling using the `nf-core/chipseq` workflow). 
+  These analyses can typically be run on your local computer and on any OS (macOS, Windows, Linux).
+- A **Linux environment** to run the pre-processing steps and peak calling (i.e. running the `nf-core/chipseq` workflow). 
+  We highly recommend using a dedicated server (typically a HPC) for this step. 
+  Technically, you can also run this workflow on Windows via _WSL2_ (we provide instructions below), but we do not recommend it for production runs. 
+
 
 ### R and RStudio
 
-::: {.tabset group="os"}
+::: {.panel-tabset group="os"}
 
 #### Windows
 
@@ -43,7 +50,7 @@ Download and install all these using default options:
 - [RTools](https://cran.r-project.org/bin/windows/Rtools/)
 - [RStudio](https://www.rstudio.com/products/rstudio/download/#download)
 
-#### Mac OS
+#### macOS
 
 Download and install all these using default options:
 
@@ -58,37 +65,124 @@ Download and install all these using default options:
 :::
 
 
+### R Packages
+
+Open RStudio and run the following: 
+
+```r
+# install BiocManager if not installed already
+if (!require("BiocManager", quietly = TRUE)){
+  install.packages("BiocManager")
+}
 
-<!--
-### Conda
+# Install all packages used
+BiocManager::install(c("GenomicRanges", "rtracklayer", "plyranges", "ChIPseeker", "profileplyr", "ggplot2", "DiffBind"))
+```
+
+
+### Conda/Mamba
 
-Open a terminal and run:
+For the command-line tools covered in the course you will need a Linux machine (or _WSL2_, if you are on Windows - see @sec-wsl).
+
+If you are an experienced Linux user, you can install/compile each tool individually using your preferred method. 
+Otherwise, we recommend doing it via the [Mamba package manager](https://mamba.readthedocs.io/en/latest/installation.html). 
+If you already use Conda/Mamba you can skip this step. 
+
+To make a fresh install of Mamba, you can run: 
 
 ```bash
-wget -q -O - https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-bash Miniconda3-latest-Linux-x86_64.sh -b
-rm Miniconda3-latest-Linux-x86_64.sh
-conda init
-conda config --add channels defaults; conda config --add channels bioconda; conda config --add channels conda-forge; conda config --set channel_priority strict
-conda install -y mamba
+wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
+bash Mambaforge-$(uname)-$(uname -m).sh
 ```
 
-Note: Windows users can use WSL2 (see @wsl).
--->
+And follow the instructions on the terminal, accepting the defaults. 
+Make sure to restart your terminal after the installation completes.
+
+These instructions also work if you're using a HPC server.
+
+
+### Nextflow
+
+We recommend having a dedicated environment for _Nextflow_, which you can use across multiple pipelines you use in the future. 
+Assuming you've already installed Conda/Mamba, open your terminal and run: 
+
+```bash
+mamba create --name nextflow nextflow
+```
+
+Whenever you want to use nextflow, you need to activate your environment with `conda activate nextflow`.
+
+
+### ChIP-seq tools
+
+For other command-line tools that we covered in the workshop, you can install them in their own conda environment:
+
+```bash
+mamba create --name chipseq
+mamba install --name chipseq idr deeptools meme homer
+```
+
+When you want to use any of them, make sure to activate your environment first with `conda activate chipseq`.
+
+
+### Windows WSL2 {#sec-wsl}
+
+:::{.callout-warning}
+We highly recommend running the raw data processing pipeline on a dedicated Linux server (typically a HPC), not directly on Windows via WSL2.
+Although you can technically run the entire pipeline on WSL2, it may be a very suboptimal way of doing so for real data.
+:::
+
+The **Windows Subsystem for Linux (WSL2)** runs a compiled version of Ubuntu natively on Windows. 
+There are detailed instructions on how to install WSL on the [Microsoft documentation page](https://learn.microsoft.com/en-us/windows/wsl/install). 
+Briefly:
+
+- Click the Windows key and search for  _Windows PowerShell_, open it and run the command: `wsl --install`.
+- Restart your computer. 
+- Click the Windows key and search for _Ubuntu_, which should open a new terminal. 
+- Follow the instructions to create a username and password (you can use the same username and password that you have on Windows, or a different one - it's your choice). 
+- You should now have access to a Ubuntu Linux terminal. 
+  This (mostly) behaves like a regular Ubuntu terminal, and you can install apps using the `sudo apt install` command as usual. 
+
+#### Setup directories
+
+After WSL is installed, it is useful to create shortcuts to your files on Windows. 
+Your `C:\` drive is located in `/mnt/c/` (equally, other drives will be available based on their letter). 
+For example, your desktop will be located in: `/mnt/c/Users/<WINDOWS USERNAME>/Desktop/`. 
+It may be convenient to set shortcuts to commonly-used directories, which you can do using _symbolic links_, for example: 
+
+- **Documents:** `ln -s /mnt/c/Users/<WINDOWS USERNAME>/Documents/ ~/Documents`
+  - If you use OneDrive to save your documents, use: `ln -s /mnt/c/Users/<WINDOWS USERNAME>/OneDrive/Documents/ ~/Documents`
+- **Desktop:** `ln -s /mnt/c/Users/<WINDOWS USERNAME>/Desktop/ ~/Desktop`
+- **Downloads**: `ln -s /mnt/c/Users/<WINDOWS USERNAME>/Downloads/ ~/Downloads`
+
+
+#### Docker for WSL
+
+We've experienced issues in the past when running _Nextflow_ pipelines from WSL2 with `-profile singularity`. 
+As an alternative, you can instead use **_Docker_**, which is another software containerisation solution. 
+To set this up, you can follow the instructions given on the Microsoft Documentation: [Get started with Docker remote containers on WSL 2](https://learn.microsoft.com/en-us/windows/wsl/tutorials/wsl-containers).
+
+Once you have _Docker_ set and installed, you can then use `-profile docker` when running your _Nextflow_ command.
+
 
-<!--
 ### Singularity
 
+Singularity is a software for running a virtual operating system locally (known as a container) and popularly used for complex bioinformatic pipelines. 
+_Nextflow_ supports the use of _Singularity_ for managing its software and we **recommend its use it on HPC servers**. 
+_Singularity_ is typically installed by your HPC admins, otherwise request that they do so. 
+
+However, if you want to run the analysis locally on your computer (again, we do not recommend you to do so), then you can install Singularity following the instructions below.
+
 ::: {.panel-tabset group="os"}
 
 #### Windows
 
-You can use _Singularity_ from the _Windows Subsystem for Linux_ (see @wsl).  
+You can use _Singularity_ from the _Windows Subsystem for Linux_ (see @sec-wsl).
 Once you setup WSL, you can follow the instructions for Linux.
 
-#### Mac OS
+#### macOS
 
-Singularity is [not available for Mac OS](https://docs.sylabs.io/guides/3.0/user-guide/installation.html#install-on-windows-or-mac).
+Singularity is [not available for macOS](https://docs.sylabs.io/guides/3.0/user-guide/installation.html#install-on-windows-or-mac).
 
 #### Linux
 
@@ -98,14 +192,14 @@ These instructions are for _Ubuntu_ or _Debian_-based distributions[^1].
 
 ```bash
 sudo apt update && sudo apt upgrade && sudo apt install runc
-CODENAME=$(lsb_release -c | sed 's/Codename:\t//')
-wget -O singularity.deb https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce_3.10.2-${CODENAME}_amd64.deb
+codename=$(lsb_release -c | sed 's/Codename:\t//')
+wget -O singularity.deb https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce_3.11.4-${codename}_amd64.deb
 sudo dpkg -i singularity.deb
 rm singularity.deb
 ```
 
 :::
--->
+
 
 
 <!--