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ARC Commander QuickStart

last updated at 2023-06-09 About this guide

In this guide we focus on how to use the ARC Commander to create your ARC and structure, store and share your data.

UserNewbie ModeTutorial

Before we can start

☑️ Please install ARC Commander
☑️ Find the command line on your system
💡 Consider reading about ARC and the ARC Commander
💡 After concluding this quickstart, consider exploring the ARC Commander manual for a more detailed usage instruction.

ARC initialization
  1. Create and navigate to a local folder, which you want to initialize as an ARC.
mkdir ~/Desktop/QuickStart cd ~/Desktop/QuickStart
  1. Initialize your ARC by executing
arc init
  1. This will create the general ARC folder structure:

arc init

Adding metadata ISA investigation

The ISA investigation (-i) workbook allows you to record administrative metadata of your project. The isa.investigation.xlsx workbook including an identifier to your ARC has been added to the project during initialization. You can update the identifier of your ARC with

arc investigation update -i QuickStartInvestigation

💡 Avoid using spaces in the identifier. Use underscores and capital letters instead.

ISA studies and assays

The ISA study (-s) and ISA assay (-a) workbooks allow you to annotate your experimental data.

  1. Add an isa.study.xlsx workbook including an identifier to your ARC with
arc study add -s QuickStartStudy
  1. Add an isa.assay.xlsx workbook including an identifier to your ARC with
arc assay add -s QuickStartStudy -a QuickStartAssay

💡 An assay must be linked to a study. If a study does not exist, it will be created automatically in this step.

subdirectories

  1. Place the data for each assay in the respective dataset folder.
Sharing your ARC DataPLANT registration and access

In case you are not a member of DataPLANT yet, please visit sign up. Afterwards, you will be granted access to DataPLANT’s DataHUB. The DataHUB allows you to share your ARCs with registered lab or project partners.

After successful registration, setup your machine for smooth ARC synchronization using the ARC Commander

  1. Allow git to store credentials on your machine.

    Windows

    git config --global credential.helper cache

    or

    git config --global credential.helper store

    MacOS

    git config --global credential.helper osxkeychain

    Linux

    git config --global credential.helper store
  2. Create and set an access token

    arc remote accesstoken get -s https://git.nfdi4plants.org

A window within your browser will open, asking for your DataPLANT Log In. In case you are already logged in, the browser will directly display a Success message to you:

ARC synchronization
  1. Synchronize your ARCs with the DataHUB using the command
arc sync
  1. If you did not connect your local ARC with a remote one so far, you can specify the remote address with the flag -r followed by an URL, e.g.,
arc sync -r https://git.nfdi4plants.org/<YourUserName>/<YourARC>
  1. In case you want to create a new remote repository at this URL, it needs to be assembled as the following example:
# https://git.nfdi4plants.org/<YourUserName>/<YourARC>
  1. If no repository exists under the given URL, the ARC Commander will produce an error ensuring that you spelled the URL correctly. To force synchronization, use
arc sync -f

  1. Check if the upload was successful by visiting your ARC at the respective URL in your browser.

Note: Alternatively, you can first create a new blank repository in the DataHUB by clicking "New project/repository" in the plus drop down menu of the navigation bar on top. Afterwards, you can sync your local ARC to the respective repository by adapting the URL to the newly generated one.

Setting a git user

Some users might want to use different signatures for different repositories, e.g. for developing software on GitHub and working on ARCs on DataPLANT's DataHUB. Besides your global git configuration, you can store the information you want to use for editing ARCs within the ARC Commander config:

arc config set -g -n "general.gitname" -v "Name of choice" arc config set -g -n "general.gitemail" -v "Email of choice"

To transfer the information from the global ARC Commander config to the local git config of the ARC use

arc config setgituser Invite collaborators

You can invite lab-colleagues or project partners to join your ARC for collaboration. While inside your ARC on the DataHUB, click on Project information -> Members in the left navigation panel. Search for registered researchers and select a role for each individually. These roles come along with different rights.
Briefly:

💡 After concluding this quickstart, you might want to explore the ARC Commander manual for a more detailed usage instruction.

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
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