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DataPLANT

General

Welcome to the ARC Commander Manual. Please explore the sections on the left to find guides on

  • Setup and Installation to use the ARC Commander,
  • Central Functions to work with your ARC, and
  • Functions to fill and work on ISA Metadata within your ARC.

A tool to make FAIR RDM easy

Section titled A tool to make FAIR RDM easy

The ARC Commander supports you in many actions on files within your ARC enabling you to sort, associate and keep track of your files.

The major function of the ARC Commander is to set up the ARC directory and put it under version-control for you. The ARC Commander creates the directory structure with the root directories “studies”, “assays”, “runs”, and “workflows” (see ARC for details). According to the design of your project, you can use the ARC Commander to create study and assay sub-directories and add the associated details and data files. While setting up the root directory structure, the ARC Commander initializes your ARC as a git repository, allowing you to track changes of your ARC and easily back-up and synchronize it with the DataHUB. This includes an efficient mechanism to keep track of your large data files. The ARC Commander makes it straight-forward to download shared ARCs from the DataHUB for collaboration.

Apart from managing the ARC as a whole in terms of file handling, the ARC Commander supervises the integrity and connections between files of your ARC. It ensures that the ARC is intact following the ARC specifications as well as the ISA model to provide machine-readability of metadata. By (automatically) registering your studies and assays including their associated meta(data) files in the isa.investigation.xlsx registry file, the ARC Commander makes the resources in your ARC identifiable and findable. It would also warn you about possible inconsistencies, such as duplicate ISA metadata files (e.g. every ARC stores only one isa.investigation.xlsx) or studies and assays that may have been added manually and not registered, yet.

What the ARC Commander does not do

Section titled What the ARC Commander does not do

Unless you actively request it to, the ARC Commander does not delete, modify or move files within your ARC. While it may help with suggestions, the ARC Commander will not guess your intentions or override your decisions. For instance, the ARC Commander will not search any (ISA) metadata or other data files in your ARC and move them into the intended folders. If such files exist somewhere in your ARC, they will simply be ignored as “additional payload” (see ARC specifications). The ARC Commander does not operate / manage your ARC automatically. You have the full control over all actions. Whenever you decide to add or link new (meta)data in your ARC or synchronize it with the DataHUB, you can do so with a few commands.

Do I have to use the ARC Commander?

Section titled Do I have to use the ARC Commander?

No. As with most tools and services developed in DataPLANT, you are not obliged to use the ARC Commander to benefit from DataPLANT’s support in FAIR RDM. However, we’d highly recommend to check it following the ARC Commander QuickStart.

The alternative would be to

  • …create the directory structure from scratch for every ARC?
  • …properly link all your isa.*.xlsx metadata and files by hand?
  • …remember where to put what metadata information?
  • …learn a bunch of git and git-lfs commands by heart?
  • …

How does it work?

Section titled How does it work?

The ARC Commander runs on current Windows, Mac and Linux operating systems. The tool is solely designed as a CLI-based software.

For details, please