Creating ARCs using ​the ARC Commander

After this basic usage instruction, you will know​:

  • - the general command line structure​

  • - the most important commands to create and validate your ARCs.​

To find the latest release of the ARC Commander, please click here

For further Information visit the ARC Commander Github Page

Although using the Commander will support you immensely in the creation of ARCs, it is optional and the ISA-TAB excel sheets can still be filled out manually.​

General command line structure

arc <object> <subcommand-verb> <subcommand-verb-args> where object is either:​
  • - <investigation> or its sub-objects​

  • - <study> or its sub-objects​

  • - <assay>

  • - <configuration>

and

subcommand-verb models what to do with the object.​

Initialize ARC​

Navigate to a folder in which you want to initialize an ARC. Open the a Command Prompt (via typing search for 'cmd' on windows or 'Terminal on MacOS') in the folder address and press Enter. Use

arc init

to create the basic ARC folder structure.

Creating investigations

Each ARC includes an isa.investigation file that serves as central information registry.

To generate such a file use

arc i create

This will open an editor asking for basic investigation information to create an ISA-TAB conform Excel file. Each investigation file MUST have a unique Identifier.

Registering ARC​ objects

To register persons, publications, factors, protocols, … use arc <object> register:

arc investigation (i) person register arc i publication register arc study (s) factor register arc s protocol register

This transports information directly into the isa.investigation.xlsx file

Adding objects to an ARC​

arc <object> add

The command arc add lets you combine arc init and arc register. It will create a new <object> in the ARC and subsequently register it with the passed arguments.

Removing objects from an ARC

arc <object> remove

The command arc remove results in the exact opposite! It lets you combine arc unregister and arc delete, deleting the <object> from the ARC file structure and the ARC’s registry.

Initialize ARC​

Navigate to a folder in which you want to initialize an ARC. Open the a Command Prompt (via typing search for 'cmd' on windows or 'Terminal on MacOS') in the folder address and press Enter. Use

arc init

to create the basic ARC folder structure.

Editing and updating ARC​ objects

Edit <objects> using

arc <object> <sub-object> edit

e.g. arc i person edit Without further arguments an editor opens that asks for the person that should be edited. If the person exists, another editor opens to edit the information.


arc <object> <sub-object> update

To avoid editor pop ups, also the command arc <object> <sub-object> update can be used, e. g. arc i person edit arc i person update –l Doe –f John --address 'Musterstraße 1, 12345 Musterstadt'

Listing ARC​ contents

To list registered <objects>, use

arc <object> list

This will show you registered persons, publications, assays, … of an investigation or a study. For a detailed usage instruction, please click here.