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.
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.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.
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.
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
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.
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.
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.
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'
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.