ARC Commander QuickStart

This document is work in progress. If you experience any inconsistencies, have questions or would like to suggest additions, please feel free to contact us or open an issue in our Helpdesk.

We are very happy that you chose our tools and infrastructure to create and share your own ARCs. In this QuickStart we focus on how to use the "ARC Commander" to store and share your data.

• Environment and setup
  • The command line
  • Required software
• ARC initialization
• Adding metadata
  • ISA investigation
  • ISA studies and assays
• Sharing your ARC
  • DataPLANT registration and access
  • ARC synchronization
  • Setting a git user
  • Invite collaborators

• Most of this Quickstart (especially the section ARC initialization) is based on the command line (Windows: powershell; Linux and Mac: terminal).
• The following picture shows exemplarily how to open a powershell on windows by entering powershell into the explorer path:

• Text formatted as code blocks represents commands to copy/paste into the command line:

• Prerequisites for using the ARC Commander are git and git LFS

Note: If this is your first time using git on this computer, you need to set your git user name and email address. These are needed for displaying them on the git commits. You can update the settings with

You can check the configuration with

• Please download the latest version of the ARC Commander for your operating system and install it according to these instructions.

• Check if the ARC Commander is functional by displaying the ARC commander version and help menu:

1. Create and navigate to a local folder, which you want to initialize as an ARC.

2. Initialize your ARC by executing

3. This will create the general ARC folder structure:

The ISA investigation (-i) workbook allows you to record administrative metadata of your project. Add the isa.investigation.xlsx workbook including an identifier to your ARC with

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

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

2. Add an isa.assay.xlsx workbook including an identifier to your ARC with

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

• The ARC Commander will add a subdirectories to the studies and assays folder. Your ARC should look similar to this now:

• These steps can be repeated to add as many studies and assays as needed. Accordingly, more subdirectories will be added. Multiple assays can be grouped in a study when the same StudyIdentifier is used.

3. Place the data for each assay in the respective dataset folder.

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:

1. Synchronize your ARCs with the DataHUB using the command

2. 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.,

3. In case you want to create a new remote repository at this URL, it needs to be assembled as the following example:

4. 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

5. 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.

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:

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

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:

• Guests: 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.

Note: A detailed usage instruction for the ARC Commander can be found here.

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