Home Fundamentals Research Data Management FAIR Data Principles Metadata Ontologies Data Sharing Data Publications Data Management Plan Version Control & Git Public Data Repositories Persistent Identifiers Electronic Lab Notebooks (ELN) DataPLANT Implementations Annotated Research Context User Journey ARC specification ARC Commander QuickStart QuickStart (Experts) Swate QuickStart Walk-through Best Practices For Data Annotation DataHUB DataPLAN Ontology Service Landscape ARC Commander Manual Setup Git Installation ARC Commander Installation Windows MacOS Linux ARC Commander DataHUB Access Before we start Central Functions Initialize Clone Connect Synchronize Configure Branch ISA Metadata Functions ISA Metadata Investigation Study Assay Update Export ARCitect Manual Installation - Windows Installation - macOS Installation - Linux QuickStart QuickStart - Videos ARCmanager Manual What is the ARCmanager? How to use the ARCmanager Swate Manual Swate Installation Excel Browser Excel Desktop Windows – installer Windows – manually macOS – manually Organization-wide Core Features Annotation tables Building blocks Building Block Types Adding a Building Block Using Units with Building Blocks Filling cells with ontology terms Advanced Term Search Templates File Picker Expert Features Contribute Templates ISA-JSON DataHUB Manual Overview User Settings Generate a Personal Access Token (PAT) Projects Panel ARC Panel Forks Working with files ARC Settings ARC Wiki Groups Panel Create a new user group Data publications Passing Continuous Quality Control Submitting ARCs with ARChigator Track publication status Use your DOIs Guides ARC User Journey Create your ARC ARC Commander QuickStart ARC Commander QuickStart (Experts) ARCitect QuickStart Annotate Data in your ARC Annotation Principles ISA File Types Best Practices For Data Annotation Swate QuickStart Swate Walk-through Share your ARC Register at the DataHUB DataPLANT account Invite collaborators to your ARC Sharing ARCs via the DataHUB Work with your ARC Using ARCs with Galaxy Computational Workflows CWL Introduction CWL runner installation CWL Examples CWL Metadata Recommended ARC practices Syncing recommendation Keep files from syncing to the DataHUB Working with large data files Adding external data to the ARC ARCs in Enabling Platforms Publication to ARC Troubleshooting Git Troubleshooting Contribute Swate Templates Knowledge Base Teaching Materials Events 2023 Nov: CEPLAS PhD Module Oct: CSCS CEPLAS Start Your ARC Sept: MibiNet CEPLAS Start Your ARC July: RPTU Summer School on RDM July: Data Steward Circle May: CEPLAS Start Your ARC Series Start Your ARC Series - Videos Events 2024 CEPLAS ARC Trainings – Spring 2024 MibiNet CEPLAS DataPLANT Tool-Workshops Frequently Asked Questions

Before we start

last updated at 2023-06-14

After the setup steps, you're all set and ready to start using the ARC Commander. 🎉

💡 We recommend trying the quickstarts for your first steps with the ARC Commander.

💡 After the quickstarts, we strongly recommend to read the in-depth ARC Commander Manual here.

Notes on ARC Commander Guides Different Routes to add Metadata

Using the ARC commander, most metadata information (e.g. the title or identifier of your investigation) can theoretically be entered solely by using the shell.

For instance, the following command would create an investigation with the identifier "MyInv001" and title "My Investigation 001":

arc investigation create --identifier "MyInv001" --title "My Investigation 001"

If no arguments are supplied, a text editor may pop up asking you for suitable metadata values. For instance, the command

arc investigation create

will open a text editor and (amongst other metadata keys) allow you to enter

Identifier: #A concise name given to the investigation Title: #A textual description of the investigation Description:

After entering the required values, you can save and close the editor.

ARC Commander's Help Menu

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:

arc --help arc investigation --help arc investigation create --help arc study --help arc study add --help arc assay remove --help

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 .
Contribution Guide 📖
✏️ Edit this page