System

Installation

Install OakVar.

pip install oakvar

Note for open-cravat users

OakVar supports backward compatibility with open-cravat and thus open-cravat should be first removed before installing OakVar by pip uninstall open-cravat. open-cravat can simply be restored by removing OakVar by pip uninstall oakvar and installing open-cravat by pip install open-cravat. There is no side-effect of doing this switch unless you share open-cravat modules with OakVar as described below.

OakVar does not share system files with nor transfer system configuration from open-cravat. OakVar's default modules directory is different.

OakVar is backward-compatible with open-cravat modules. If you have been using open-cravat and want to continue to use open-cravat modules with OakVar, you can do so by setting OakVar modules directory to point to that of open-cravat with ov system md command. Please keep in mind that OakVar has its own updated versions for some of open-cravat modules, so if you are sharing the same modules directory between OakVar and open-cravat, ov module update may break oc-compatibility of some of the updated modules.

Setup

ov system setup will set up OakVar with sane defaults.

Setup process can be customized with a setup file or environment variables, which can be useful in automated deployment.

System modules are automatically installed with ov system setup. If you want to install additional modules as a part of ov system setup process, you can use --modules option as follows.

ov system setup --modules clinvar biogrid

Setup with a file

A setup file in yaml format can be used. System configuration fields which are missing in the setup file will be filled with sane defaults. Setup with a file with custom locations for modules and logs can be done as

ov system setup -f setup.yaml

where setup.yaml is

modules_dir: ~/oakvar_modules
logs_dir: ~/oakvar_logs

The filename of the setup file does not have to be setup.yaml.

You can specify your OakVar store account email and password in setup.yaml as follows:

ov_store_email: YOUR_EMAIL
ov_store_pw: YOUR_PASSWORD

Additional modules can be specified as well in the setup file as follows.

modules:
- clinvar
- biogrid

Setup with environment variables

All system configuration fields can be overridden with environment variables. To override a system config field, set the environment variable OV_ + upper-cased field name to a desired value. For example,

System configuration field	Environmental variable
sys_conf_path	OV_SYS_CONF_PATH
root_dir	OV_ROOT_DIR
modules_dir	OV_MODULES_DIR
log_dir	OV_LOG_DIR
jobs_dir	OV_JOBS_DIR
conf_dir	OV_CONF_DIR
gui_port	OV_GUI_PORT

The custom setup in the previous section can be done using environmental variables as

export OV_MODULES_DIR=~/oakvar_modules
export OV_LOGS_DIR=~/oakvar_logs
ov system setup

Another example is installing system files in a custom directory.

export OV_ROOT_DIR=/data/oakvar
ov system setup

This will install OakVar system files at /data/oakvar.

Using environmental variablse for setup can be useful in deploying OakVar with Docker containers.

Clean setup

If you experience any problem and want to do clean installation of OakVar, ov system setup --clean provides such clean installation. It will reset the system and user configuration files. --clean still will not delete modules, jobs, logs, and conf folders. modules have downloaded modules and users should manually delete this folder if they really want, because this folder can take a lot of time to recreate. jobs, logs, and conf folders have just contents.