Merge pull request #15 from jsaintvanne/doc-ju

Doc ju

.Rprofile

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+source("renv/activate.R")

.github/workflows/publish.yml

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+# Workflow for rendering and deploying quarto site to GitHub Pages
+# Based on the GitHub example static content deploy action
+name: 🚀 Deploy Quarto site to Pages
+
+on:
+  workflow_dispatch:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["doc-ju"]
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Single deploy job since we're just deploying
+  build-deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-20.04
+    steps:
+      - name: 📂 Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🚚 Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install GDAL, UDUNITS2
+        run: sudo apt update; sudo apt install libgdal-dev libudunits2-dev
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.2.0'
+
+      - name: Install R Dependencies
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          cache-version: 1
+
+      - name: 🎉 Deploy to GitHub Pages
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+

.gitignore

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-.swp
-.*.swp
+.*.swp
+.Rproj.user
+.Rhistory
+/.quarto/*
+./docs/*
+docs/*
+_freeze/*

README.md

@@ -3,6 +3,7 @@
 [![Docker Stars](https://img.shields.io/docker/stars/workflow4metabolomics/galaxy-workflow4metabolomics.svg?maxAge=2592000)](https://cloud.docker.com/u/workflow4metabolomics/repository/docker/workflow4metabolomics/galaxy-workflow4metabolomics)
 [![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io)
 [![Build Status](https://travis-ci.org/workflow4metabolomics/xcms.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/xcms)
+[![example workflow](https://github.com/jsaintvanne/workflow4metabolomics/actions/workflows/publish.yml/badge.svg)](https://github.com/jsaintvanne/workflow4metabolomics/actions/workflows/publish.yml/badge.svg)
 
 ![workflow](/images/logo/logo-ifb-mono-metabohub_2.1_SD_150px.png)
 
@@ -63,3 +64,70 @@ Guidelines
 ----------
 
 - [Writing a tool](GUIDELINES.md#writing-a-tool)
+
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+[![example workflow](https://github.com/jsaintvanne/workflow4metabolomics/actions/workflows/publish.yml/badge.svg)](https://github.com/jsaintvanne/workflow4metabolomics/actions/workflows/publish.yml/badge.svg)
+
+
+![workflow](/images/logo/logo-ifb-mono-metabohub_2.1_SD_150px.png)
+
+
+# How to contribute to the documentation?
+
+If you want to contribute to this documentation on Workflow4Metabolomics, you will need to have a Github account first. Indeed, every files of this documentation are pushed in github and will stay there. To be able to accept new things from different people, we need to set some steps to follow:
+
+1. Start by forking the repository: 
+
+![fork this thing](../images/fork_picture.png)
+
+2. Then you can work directly on github or clone the repository to your local environment (link clone)
+
+3. Once you have saved your changes (with commits pushed on your forked repository) there should be an orange band like the following to ask for a pull request ![This is my PR](../images/pull_request_picture.png)
+
+4. You just have to open this pull request and we will review it in order to validate it. Please think about explaining your changes in your newly opened pull request for us to know what is is all about. Once the pull request is aprouved, changes will appear on the website.
+
+
+### Tip: Adding information on a page
+
+If you just want to add some information on an existing page or update some deprecated information, it is quite easy to do. 
+During the previous step n°2, you just have to open the file you want to change (on Github or on your local computer if cloned), make your changes and then save it in a new commit.
+When your commit is saved with changes, the orange band will appear and you can proceed with the previous step n°3 (or continue by updating further content). 
+
+### Tip: Creating a new page
+
+It is also possible to add a new page on the website. This is different from the previous point because you will need to change the `_quarto.yml` file also. To be able to do this, start with thinking about *Where can my new page be on the website? A new item in the menu? A new tab in an existing one?*. 
+Then in the file named `_quarto.yml` find the good part and add it with these information: 
+```{R}
+ - text: "Tools"
+        icon: "tools"
+        menu: 
+          - text: "Tool 1"
+            href: tool1.qmd
+          - text: "My new tool"
+            href: mynewtool.qmd
+```
+
+As you can see, you now need to create your new `mynewtool.qmd` file. In this file you can write all you want (in accordance with where it will be in the website of course!).
+After all this is completed, as in the previous tip, just save and open the pull request explaining what you want to add for us to be able to evaluate its accordance to the website.

W4E/w4e2014.qmd

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+---
+title: "Workflow4Experimenters 2014"
+year: 2014
+place: Lyon, France
+date: ??
+speakers: 
+---

W4E/w4e2015.qmd

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+---
+title: "Workflow4Experimenters 2015"
+year: 2015
+place: Roscoff, France
+date: 21-25 September
+speakers: 
+---

W4E/w4e2016.qmd

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+---
+title: "Workflow4Experimenters 2016"
+year: 2016
+place: Roscoff, France
+date: 28 November - 2 December
+speakers: 
+---
+
+W4E 2016
+options de configuration Ouvert
+
+
+Workflow4Experimenters (W4E) course 2016
+
+Using Galaxy and the Workflow4metabolomics infrastructureto analyse metabolomics data
+
+
+
+Overview: Pre-processing, statistical analysis, and annotation of metabolomics data is a complex task. The Workflow4metabolomics online infrastructure provides a user-friendly and high-performance environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, and NMR analysis (Giacomoni et al, 2015).
+
+Goals: During this one-week course, participants will learn how to use the W4M infrastructure to analyze their own dataset.Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.
+
+Target audience: LC-MS, GC-MS and NMR experimenters (e.g. biologists, chemists)
+
+Date: Monday 28th November 2016 to Friday 2nd December, 2016
+
+Location: ABiMS platform (Roscoff, France)
+
+
+
+
+
+Les cours auront lieu à l’Hôtel de France :
+
+  Place Georges Teissier, Roscoff, 29680
+Google Maps
+Hôtels : Vous serez logé dans un des deux hôtels suivants. Nous vous enverrons les codes d'accès quelques jours avant la formation.
+
+Gulf Stream :
+400, rue Marquise de Kergariou, Roscoff, 29680
+Google Maps
+Hôtel de France:
+Place Georges Teissier, Roscoff, 29680
+Google Maps
+Plans
+Plan de Roscoff
+Roscoff sur maps.google.fr
+Venir à la station biologique de Roscoff
+
+
+
+
+Contact: [email protected]

W4E/w4e2017.qmd

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+---
+title: "Workflow4Experimenters 2017"
+year: 2017
+place: Paris, France
+date: 29 May - 2 June
+speakers: Tim Ebbels, Steffen Neumann, Ralf Weber
+---

W4E/w4e2018.qmd

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+---
+title: "Workflow4Experimenters 2018"
+year: 2018
+place: Paris, France
+date: 8-12 October
+speakers: Julien Boccard, Christoph Steinbeck
+---
+
+Overview
+Processing, statistical analysis, and annotation of metabolomics data is a complex task for experimenters since it involves many steps and requires a good knowledge of both the methodology and software tools. The Workflow4metabolomics.org (W4M) online infrastructure provides a user-friendly and high-performance environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, and NMR analysis. Such features are of major values for teaching computational metabolomics to experimenters, and previous courses using W4M since 2014 have been very successful.
+
+Pre-Registration are closed now !!
+  Goals: During this one-week course, participants will learn how to use the W4M infrastructure to analyze their own dataset. Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.
+
+Date: Monday 8th  to Friday October 12th  2018
+
+Costs: 900 € for academic and 2000 € for private institution to cover expenses for trainers (12), organization, materials and meals
+
+Including : Lunch, coffee break, pedagogic support and the Thursday social event
+
+Not included : travel expenses, accomodation and 3 diners (Monday, Tuesday, Wednesday)
+
+Target audience: LC-MS, GC-MS, NMR, FIA-MS and DI-MS  experimenters (e.g. biologists, chemists).
+
+Materials: Participants will use their laptop to perform the analysis on their W4M account. All presentations, reference datasets and workflows will be available online.
+
+Tutors: Each participant will be paired with a tutor who will help him/her prepare the data and assist him/her during each analysis step.
+
+Location : Pasteur Institute - Paris
+
+Language: English
+
+Number of attendees: 25 max.
+
+Keynote speakers: Julien Boccad (University of Geneva, Switzerland), Christoph Steinbeck (Friedrich Schiller University, Jena, Germany)
+
+Sponsors: ELIXIR, French Bioinformatics Institute (IFB), French Infrastructure for Metabolomics and Fluxomics (MetaboHUB), Francophone Network for Metabolomics and Fluxomics (RFMF)
+
+Program
+
+![Planning 2018](images/planning_w4e_2018.jpg)
+
+Organizing committee
+ELIXIR-France (IFB) : Christophe Caron, Gildas Le Corguillé
+
+MetaboHUB : Etienne Thévenot, Franck Giacomoni, Marie Tremblay-Franco
+
+LABERCA : Yann Guitton
+
+Institut Pasteur : Fabien Mareuil
+
+Conference Lodging
+We provide a list of hotel near to the school location (Pasteur Institute). There is also many other hotels in Paris!
+
+  Korner** 4 minutes) / 54 rue Falguière - 75015 Paris
+Aberotel*** (9 minutes) / 24 rue Blomet - 75015 Paris
+Hotel Lecourbe*** (11 minutes) / 28 rue Lecourbe - 75015 Paris
+
+Hosted by Pasteur Institute
+
+Institut Pasteur

W4E/w4e2020.qmd

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+---
+title: "Workflow4Experimenters 2020"
+year: 2020
+place: Brussels, Belgium
+date: 3-7 February
+speakers: Susanne Mar, Ralf Weber, Nathalie Poupin
+---
+Overview
+Processing, statistical analysis, and annotation of metabolomics data is a complex task for experimenters since it involves many steps and requires a good knowledge of both the methodology and software tools. The Workflow4metabolomics.org (W4M) online infrastructure provides a user-friendly and high-performance environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, FIA and NMR analysis. Such features are of major values for teaching computational metabolomics to experimenters, and previous courses using W4M since 2014 have been very successful.
+
+Pre-Registration are closed now - Don't hesitate to contact us if you have any questions or requests (contact AT workflow4metabolomics.org)
+
+![W4E 2020 affiche](images/W4E_2020_affiche.png)
+
+Goals: During this one-week course, participants will learn how to use the W4M infrastructure to analyze their own dataset. Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.
+
+Date: from Monday 3th, (lunch time)  to Friday Febrary 7th (lunch time) 2020
+
+Costs: 900 € for academic and 2000 € for private institution (to cover expenses for trainers, organization, materials and meals)
+
+Including : Lunch, coffee break, pedagogic support and the Thursday social event
+
+Not included : travel expenses, accomodation and 3 diners (Monday, Tuesday, Wednesday)
+
+Target audience: LC-MS, GC-MS, NMR, FIA-MS and DI-MS  experimenters (e.g. biologists, chemists).
+
+Materials: Participants will use their laptop to perform the analysis on their W4M account. All presentations, reference datasets and workflows will be available online.
+
+Tutors: Each participant will be paired with a duo of tutors (preprocessing / statistics experts) who will help him/her preparing data and assist him/her during each analysis step.
+
+Location :  Centre For Fine Arts (BOZAR), rue Royale n°10 to 1000 - Brussels (Belgium)
+
+Language: English
+
+Number of attendees: 25 max.
+
+Keynote speakers: Dr S. Marr (Leibniz Institute of Plant Biochemistry, Germany), Dr R. Weber (Phenome Centre Birmingham, Great Britain) and Dr N. Poupin (Unité Toxalim, INRA Toulouse, France)
+
+Sponsors: ELIXIR, French Bioinformatics Institute (IFB), French Infrastructure for Metabolomics and Fluxomics (MetaboHUB), Francophone Network for Metabolomics and Fluxomics (RFMF), Université Libre de Bruxelles (ULB) and Fonds de la Recherche Scientifique (FNRS)
+
+Program
+
+![Planning 2020](images/planning_w4e_2020.png)
+
+Scientific committee
+Université Libre de Bruxelles: Cédric Delporte, K. Triqueneaux (organization)
+
+Université de Liège: Pascal De Tullio
+
+ELIXIR-France (IFB): Gildas Le Corguillé, Valentin Saint-Leger (organization)
+
+MetaboHUB: Marie Tremblay-Franco, Mélanie Pétéra, Cécile Canlet, Binta Diemé, Franck Giacomoni and the W4M coreteam
+
+INRA Unité de Nutrition Humaine: Céline Dalle
+
+LABERCA Nantes: Yann Guitton
+
+
+
+Conference Lodging
+We will provide a list of hotels near to the school location (Centre For Fine Arts). There is also many other hotels in Brussels!
+
+
+
+Hosted by Université Libre de Bruxelles and Centre For Fine Arts
+
+![](images/ulb_logo.png)
+