Start Your ARC Workshop Series

Session 02 - Build your ARC
May 31st, 2023


Dominik Brilhaus - CEPLAS Data Science

Goals

  • Create your first ARC
  • Add data to your ARC
  • Share the ARC

Legend

💻 = Locally (on your machine)

🌐 = Remote (in the DataHUB)

Info in <brackets> are placeholders - please replace with proper info

Part 0: Check-in

Installation

Open a terminal and one after the other execute

git --version

git-lfs --version

arc --version

💡 If you see a warning at any of these, let me know.

Config

git config --global --get-regexp user

💡 If this does not display your user name and email, you need to configure git.

Have a simple text editor ready

  • Windows Notepad
  • MacOS TextEdit

Recommended text editors with code highlighting:

Create a fresh folder for your ARCs

For this workshop, create a new folder somewhere on your machine where you want to store ARCs, e.g. on the desktop:

  • C:\Users\<username>\Desktop\workshop-arcs (windows)
  • ~/Desktop/workshop-arcs (mac)

Download the demo data

git clone "https://demo-user:1_eznikmzxzARAbUxxnF@git.nfdi4plants.org/teaching/demo-arc_level0.git"

Part 1: Hands-on with demo data

Your fresh ARC folder

  1. 💻 Create a new folder, which you want to initialize as an ARC.
  2. 💻 Open the command line inside the folder or navigate via command line to that folder.

For example:

mkdir -p ~/Desktop/workshop-arcs/arc-demo
cd ~/Desktop/workshop-arcs/arc-demo

Initiate the ARC folder structure

arc init

Create an investigation

arc investigation create -i TalinumPhotosynthesis

Add a study

arc study add -s talinum_drought

Add assays

arc assay add -s talinum_drought -a rnaseq
arc assay add -s talinum_drought -a metabolomics

Upload your local ARC to the DataHUB

arc sync -r https://git.nfdi4plants.org/<username>/arc-demo

Sort the demo data into the ARC

Identify "raw dataset(s)" and "protocols" and move them to the proper subfolders in the ARC.

Sync your ARC to the DataHUB

To save the changes, sync the ARC to the DataHUB including a message.

arc sync -m "sorted the demo data"

Invite a collaborator 🌐

  1. Click on Project Information in the left navigation panel

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  1. Click on Members

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  1. Click on Invite members

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  1. Search for potential collaborators

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  1. Select a role

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Choosing the proper role

Guest
Have the least rights. This is recommended for people you ask for consultancy.

Developers
The choice for most people you want to invite to your ARC. Developers have read and write access, but cannot maintain the project on the DataHUB, e.g. inviting others.

Maintainers
Gives the person the same rights as you have (except of removing you from your own project). This is recommended for inviting PIs or group leaders allowing them to add their group members for data upload or analysis to the project as well.

A detailed list of all permissions for the individual roles can be found here

Contributors

Slides presented here include contributions by

Title slide to class

## Open the online notepad > link removed from online presentation ## Screen-sharing during the workshop > link removed from online presentation :bulb: Any windows volunteer?

Source to slide(s)

../../bricks/datahub_invite-collaborators.md

Source to slide(s)

../../bricks/datahub_choose-collaborator-role.md