Installing through OakVar Store
The OakVar Store is where OakVar's modules are registered, found, and distributed. If you used OpenCRAVAT, OpenCRAVAT's modules are also available through OakVar Store if there is no updated OakVar version of the same module exists. To know which modules are available through the OakVar Store, do
ov module ls -a
This will list the OakVar modules available through the OakVar Store. To know more details of a specific module, do
ov module info module_name # module_name such as clinvar
To install modules, do
ov module install module_name [module_name] ...
A regular expression can be given as module_name. Thus,
ov module install clin.*
will install all modules the name of which starts with
Installing through GitHub
ov module install can accept a GitHub URL as module_name. Thus, OakVar can now install custom modules directly from GitHub. It is as easy as simply giving the URL of the folder of the module on GitHub to
ov module install. Let's say you have a custom module hosted on the
dev branch of your GitHub repo
yourorganization/yourrepo in the following folder:
https://github.com/yourorganization/yourrepo/ oakvar_modules/ annotators/ awesomeannotator/ awssomeannotator.py awssomeannotator.yml awssomeannotator.md data/ awesomeannotator.sqlite
Your colleagues can install
awesomeannotator module with the following command.
ov module install \ https://github.com/yourorganization/yourrepo/\ tree/dev/oakvar_modules/annotators/awssomeannotator
will download the content of only the
annotator folder in the
dev branch of the repository, figure out that the module is an
annotator, and put the
awesomeannotator module under the appropriate
annotators category folder inside your system's OakVar modules root directory.
This way, your custom module under development can be easily shared with your colleagues.