Create an ARC

So, where do I start? What is an ARC? And how do I create one?

An ARC represents an entire investigation. At the top level, it includes directories named “studies,” “assays,” “workflows,” and “runs,” along with an investigation metadata table that holds all administrative metadata.

It follows a very specific structure to be easily readable by machines 🤖. While it can be created by hand it is faster to use some tooling!

ARCitISA installation

If ARCitISA is not yet installed on your computer,

please follow these instructions to install ARCitISA

Installing Git and Git LFS

Note

ARCitISA depends on Git and Git LFS. If not already installed, these need to be installed separately.

Windows

1. Download the Git installer for Windows from https://git-scm.com.
2. Open the installer and follow the installation instructions
3. During the installation, make sure to include Git LFS (Large File Support)

macOS

1. Open a Terminal

2. (Optional, if homebrew is not yet installed:) Install the package manager homebrew via

   /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

3. Install Git via homebrew with

   brew install git

4. Install Git LFS via homebrew with

   brew install git-lfs

5. Initialize Git LFS via

   git lfs install

Linux

1. Open a Terminal

2. Update the package manager apt via

   sudo apt update

3. Install Git via apt with

   sudo apt-get install git

4. Install Git LFS via apt with

   sudo apt-get install git-lfs

5. Initialize Git LFS via

   git lfs install

Tip

For more details or alternatives, check out the documentation of Git and Git LFS.

Installing ARCitISA

Windows

1. Head to the ARCitISA’s GitHub release page.

2. Under “Assets” download the latest release for Windows (ARCitISA-x.x.x Setup.exe).

3. In Windows Explorer, start ARCitISA-x.x.x Setup.exe to install ARCitISA

4. Once started, you see a Windows Defender warning. To proceed, click More info and then Run anyway.

   

5. Windows Defender Firewall further asks you to allow network communication. This enables communication with the DataHUB.

   

macOS

1. Head to the ARCitISA’s GitHub release page.

2. Download the macOS installer ARCitISA-x.x.x.dmg for your platform (Intel: x64 or Apple Silicon: arm64).

3. Double-click the installer ARCitISA-x.x.x.dmg and move the app to your Applications folder.

Unidentified developer

When starting ARCitISA for the first time, you are warned about an unidentified developer.

Please navigate to the Privacy & Security panel in your System Settings to Open Anyway.

Accept incoming network connections

Every time you start the ARCitISA, you are asked to accept incoming network connections.

This enables communication with the DataHUB.

Linux

1. Install additional dependencies via

   sudo apt-get update
   sudo apt-get install libgtk-3-0 libnotify4 xdg-utils libsecret-1-0

   Note

   On some linux distributions you have to run sudo apt --fix-broken install afterwards.

2. Head to the ARCitISA’s GitHub release page.

3. Download the Linux DEB package ARCitISA-x.x.x_amd64.deb.

4. Install ARCitISA

   sudo dpkg -i ./ARCitISA-x.x.x_amd64.deb

5. Start the ARCitISA via

   arcitisa

   Admin privileges

   apt-get install and dpkg -i often require admin privileges, since they write into system directories. You can circumvent this problem by local installations in folders where you have permission, e.g.

   dpkg-deb -x ./ARCitISA-x.x.x_amd64.deb $HOME/arc

   would install the ARCitISA in a folder in your home directory. You can then add it to your path via

   export PATH="$HOME/arc/ARCitISA:$PATH"

   To install git, git-lfs, libgtk-3-0, libnotify4, xdg-utils and libsecret-1-0, if they are not already installed, you can use apt download, which gives you the .deb files for their installations.
   From there you can proceed the same as written above for the ARCitISA. apt download does not resolve package dependencies, so you may have to resolve them manually.

Create a new ARC

1. Start the ARCitISA app.

2. In the dropdown on top click on “Create new ARC”.

   

3. Select an identifier for your ARC.

   

   To keep it simple, I call my ARC “AthalianaColdStressSugar”

   Tip

   • Use a short acronym
   • Avoid spaces and special characters in your ARC’s name
   • Avoid administrative metadata (name, data, etc.)
   • Use a combination of keywords, maybe a grant number

4. Click Create new ARC

5. Select a location and click “open”.

6. ARCitISA creates the base ARC folder on your computer and opens it right away.

   • DirectoryAthalianaColdStressSugar

     • notes
     • isa.investigation.xlsx
     • assays
     • runs
     • studies
     • workflows

Your ARC’s name

By default, your ARC’s name will be used:

1. For the ARC folder on your computer.
2. As the investigation identifier.