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ARC Commander QuickStart

This guide introduces the ARC Commander, a command line tool to create, edit and share you ARC. It requires some experience with the command line (command prompt, shell, terminal,…).

Before using the ARC commander, please install Git, Git-LFS and ARC Commander and setup access to your DataHUB account.

  1. Install and setup Git and Git-LFS

    In order to use the ARC Commander, Git (version ≥ 2.32.0) and Git LFS must be installed on your computer.

    Download and install Git and Git LFS

    Section titled Download and install Git and Git LFS

    Please install Git and Git LFS

    • On Windows Git LFS may already be installed during your Git installation
    • For macOS we recommend to install via homebrew as described on the site above

    To check, that Git and Git LFS are installed on your computer, open a new command prompt or terminal and execute the following two commands. These should display the installed version.

    Terminal window
    git --version
    Terminal window
    git-lfs --version

    After installation of Git LFS you must run the following command once to make sure Git LFS is initialized on your system.

    Terminal window
    git lfs install

    Git always signs “commits” with a user name and e-mail address. These are then also used by the DataHUB to associate the commits to your user account.

    To add your user name and email address to the git configuration on your computer, run the following two commands in a command prompt or terminal. Make sure to replace “Your DataHUB Name” and “Your DataHUB Email Address” with your information from the DataHUB.

    1. Your name
    Terminal window
    git config --global user.name "Your DataHUB Name"
    1. Your email address
    Terminal window
    git config --global user.email "Your DataHUB Email Address"

    Run this command to display your user configuration

    Terminal window
    git config --global --get-regexp user
  2. Install ARC Commander

    In order to use the ARC Commander, Git (version ≥ 2.32.0) and Git LFS must be installed on your computer.

    Download and install Git and Git LFS

    Section titled Download and install Git and Git LFS

    Please install Git and Git LFS

    • On Windows Git LFS may already be installed during your Git installation
    • For macOS we recommend to install via homebrew as described on the site above

    To check, that Git and Git LFS are installed on your computer, open a new command prompt or terminal and execute the following two commands. These should display the installed version.

    Terminal window
    git --version
    Terminal window
    git-lfs --version

    After installation of Git LFS you must run the following command once to make sure Git LFS is initialized on your system.

    Terminal window
    git lfs install

    Git always signs “commits” with a user name and e-mail address. These are then also used by the DataHUB to associate the commits to your user account.

    To add your user name and email address to the git configuration on your computer, run the following two commands in a command prompt or terminal. Make sure to replace “Your DataHUB Name” and “Your DataHUB Email Address” with your information from the DataHUB.

    1. Your name
    Terminal window
    git config --global user.name "Your DataHUB Name"
    1. Your email address
    Terminal window
    git config --global user.email "Your DataHUB Email Address"

    Run this command to display your user configuration

    Terminal window
    git config --global --get-regexp user
  3. Register for a DataPLANT account

    With a DataPLANT account you can use the DataHUB and share your ARC for collaboration.

    Please register here.

    During the registration you can “Choose your role in DataPLANT”:

    • DataSteward
      • Member of / associated to DataPLANT
      • Teaches DataPLANT tools and services to community members
    • Developer
      • Member of / associated to DataPLANT
      • Develops DataPLANT tools and services
    • Member
      • Other member of DataPLANT
    • User
      • User who want to use the DataPLANT tools and services

    If you want to adjust your account settings, simply click the login icon in the navigation bar on this site.

    • In the tab “Password” you can modify your password.
    • In the tab “Authenticator” you can set up Two Factor Authentication (2FA).
  4. Setup DataHUB access

    The DataHUB allows you to share your ARCs with registered lab or project partners. After registration, you need to setup the ARC Commander for smooth ARC synchronization between your computer and the DataHUB.

    Enable Git to store credentials on your computer

    Section titled Enable Git to store credentials on your computer

    Open a command prompt or terminal and execute the following command(s)

    Terminal window
    git config --global credential.helper store
    Terminal window
    git config --global credential.helper osxkeychain

    Receive and store a DataHUB access token

    Section titled Receive and store a DataHUB access token
    Terminal window
    arc remote accesstoken get -s https://git.nfdi4plants.org

    A browser window will open asking for your DataPLANT login. After login you are asked to authorize your computer to communicate with the DataHUB. In case you are already logged in, the browser will directly display a plain Success message to you.

    Store a configurable DataHUB access token for your project

    Section titled Store a configurable DataHUB access token for your project

    Access tokens created with the ARCommander expire after two hours. To create a longer-lasting access token for your project, follow these steps:

    1. Create a project access token

      This guide shows you how to generate a Project Access Token. Project Access Token are similar to Personal Access Token, but Project Access Tokens are scoped to a project, so you cannot use them to access resources from other projects.

      1. Sign in to the DataHUB
      2. Open your Project (ARC)
      3. Navigate to ‘Settings’ (1), then ‘Access Tokens’ (2): Alt text
      4. Choose a name for your token (1), set an expiration date (optional) (2), assign a role (3), configure permissions (4), and create your token (5): Alt text
      5. Once created, you can copy the token: Alt text
    2. Store the token in your local ARC

      Terminal window
      arc remoteaccess accesstoken store --token <replaceWithYourToken>

    Once set up, you will not need to authenticate yourself (e.g., by manually retrieving a token through ‘arc remote token get’) until the token expires. When switching to another machine you have to repeat the process.

  1. Create and navigate to a local folder, which you want to initialize as an ARC, e.g. via file explorer or

    Terminal window
    mkdir AthalianaColdStressSugar
    cd AthalianaColdStressSugar
  2. Initialize your ARC by executing

    Terminal window
    arc init

This created the general ARC folder structure:

  • studies
  • assays
  • workflows
  • runs
  • isa.investigation.xlsx
  1. Add an investigation identifier (-i or --investigationidentifier)

    Terminal window
    arc investigation update -i AthalianaColdStressSugar
  2. Add a Title

    Terminal window
    arc investigation --title "Arabidopsis thaliana cold acclimation"
  3. Add a Description

    Terminal window
    arc i --description "This experiment investigates the response of Arabidopsis thaliana to cold stress by subjecting plants to low-temperature conditions and monitoring physiological, molecular, and growth-related changes. Cold-treated plants are compared with control groups grown under optimal conditions to assess stress-related markers such as changes in protein abundance, sugar content, and growth rates. The goal is to identify key molecules and physiological responses involved in cold tolerance, contributing to the understanding of plant stress adaptation mechanisms."
  4. Add Contacts

    Terminal window
    arc i person register -f Jasmine -l Beetroot
    arc i person register -f Oliver -l Sage
    arc i person register -f Viola -l Canina --email viola@plantscience.xyz
  1. Add a study with an identifier (-s, --assayidentifier)

    Terminal window
    arc study add -s AthalianaColdStress
  2. Add assays with an identifier (-a, --assay)

    Terminal window
    arc assay add -s AthalianaColdStress -a SugarMeasurement
    arc assay add -s AthalianaColdStress -a Proteomics_MS
    arc assay add -s AthalianaColdStress -a Proteomics_DataAnalysis

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

  • Directorystudies
    • DirectoryAthalianaColdStress
      • resources
      • protocols
      • isa.study.xlsx
  • Directoryassays
    • DirectorySugarMeasurement
      • dataset
      • protocols
      • isa.assay.xlsx
  • Directoryworkflows
  • Directoryruns
  • isa.investigation.xlsx
  1. Synchronize your ARCs with the DataHUB using the command

    Terminal window
    arc sync
  2. If you did not connect your local ARC with a remote one so far, you can specify the remote address (-r or --remote) followed by the DataHUB URL, e.g.,

    Terminal window
    arc sync -r https://git.nfdi4plants.org/<YourUserName>/<YourARC>
  3. If no ARC exists under the given URL, you can force (-f or --force) the ARC Commander to create it.

    Terminal window
    arc sync -f
  4. Check if the upload was successful by visiting your ARC at the respective URL in your browser.

The ARC Commander comes with a leveled help menu, that suggests suitable inputs on every level of command or subcommand. You can simply add -h or --help at the end of an ARC Commander action to display the respective help menu.

Some examples:

Terminal window
arc --help
Terminal window
arc investigation --h
Terminal window
arc investigation create --help
Terminal window
arc study --h
Terminal window
arc study add --help
Terminal window
arc assay remove --help

Here we only introduced the basic functions. After concluding this quickstart, you might want to explore the ARC Commander manual for a more detailed usage instruction.

In order to annotate the data in your ARC, explore the sections on studies and assays in the Getting Started guide. You can do this with ARCitect or Swate.