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Before we start
Central Functions
Initialize
Clone
Connect
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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?
Connect to your DataHUB
View your ARCs
Create new ARCs
Add new studies and assays
Upload files
Add metadata to your ARCs
Swate Manual
QuickStart
QuickStart - Videos
Annotation tables
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ISA-JSON
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Guides
ARC User Journey
Create your ARC
ARCitect QuickStart
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Annotate Data in your ARC
Annotation Principles
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Swate QuickStart
Swate QuickStart - Videos
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
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CWL Introduction
CWL runner installation
CWL Examples
CWL Metadata
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Keep files from syncing to the DataHUB
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Working with large data files
Adding external data to the ARC
ARCs in Enabling Platforms
Publication to ARC
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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
TRR175 Becoming FAIR
CEPLAS ARC Trainings – Spring 2024
MibiNet CEPLAS DataPLANT Tool-Workshops
TRR175 Tutzing Retreat
Frequently Asked Questions
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
- For most steps in this manual and in the guides, it is assumed, that you opened a shell or command prompt within a directory you want to initiate as an ARC
- In the shell,
arc
defines the path to the ARC Commander executable (e.g. on Windows "C:\Users\userA\programs\ArcCommander\arc.exe").
- Note that each input that contains non-literal characters must be encapsulated in "quotation marks" when entered within the shell. This also applies when using the editor for numerals that are no numbers (dates, phone numbers, etc.).
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
.