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CLI Commands

Please add -h to each command to see help for options. For example, ov run -h, ov report -h, and ov gui -h.

Setup

ov system setup [-f setup_file --email EMAIL --pw PASSWORD --clean]

setup_file is a YAML format file with setup options, such as email, password, and installation directory. For example, if oakvar_setup.yml has the following,

email: person@company.com
pw: password
modules\_dir: /path/to/directory/for/oakvar/modules

ov system setup -f oakvar_setup.yml will use the email and password in the file and install OakVar modules in the modules_dir.

Run an analysis job

ov run input_path [option ...]

Create annotation reports

ov report sqlite_file_path [option ...]

sqlite_file_path is the path to a .sqlite file produced by ov run.

Launch a GUI server

ov gui sqlite_file_path [option ...]

sqlite_file_path is the path to a .sqlite file produced by ov run.

Manage modules

List modules

ov module ls [option ...] [module_names ...]

module_names is a regular expression. For example, ov module ls -a ".*cancer.*" will list all available modules which has "cancer" in their name.

Install modules

ov module install module_names [module_name] ... [option ...]

Uninstall modules

ov module uninstall module_name [module_name] ... [option ...]

Update modules

ov module update [module_name_patterns ...] [option ...]

module_name_patterns is a regular expression.

Get information on modules

ov module info module_name [option ...]

Manage store accounts

Create a store account

ov store account create

Log in on the OakVar store

ov store login [--email EMAIL --pw PASSWORD]

Log out from the OakVar store

ov store logout

Check if logged in on the OakVar store

ov store account check

Change a store account password

ov store account change

Reset the password of a store account

ov store account reset

Delete a store account

ov store account delete

Publish modules

Pack a module for registering at the OakVar store

ov module pack module_name [-d OUTDIR --code-only --split]

-d: output directory
--code-only: only code files will be packed into a .zip file.
--split: packed files will be split into 100MB-size files.

About packing and publishing your modules, see here.

Register a module at the OakVar store

ov store register module_name [--code-url URL --data-url URL --overwrite]

Details on this command, see here.

Manage configuration

Manage modules directory

ov system md [NEW_DIRECTORY]

If NEW_DIRECTORY is not given, show the current location of OakVar modules. If given, changes the location of OakVar modules to NEW_DIRECTORY.

Show system configuration

ov config system [key value type]

If key, value, and type are not given, shows the current system configuration. If given, updates the system configuration for the key with the value of the type. For example,

ov config system modules_dir /Volumes/ExtSSD/ov_modules str

will update the modules_dir value of the system configuration. type is a Python data type, such as int, float, and str.

Utilities

Create an example input file

ov new exampleinput

oakvar_example.vcf file will be created with example variants.

Create an annotation module template

ov new module -n NAME -t TYPE

NAME: module name
TYPE: module type such as converter, mapper, annotator, 
      postaggregator, and reporter

A template for an OakVar module will be created at modules_dir/TYPEs/NAME. New module development can start with this template.

Merge analysis result database files

ov util mergesqlite

Filter analysis result database files

ov util filtersqlite

Show analysis result database file information

ov util sqliteinfo --fmt [json(default)|yaml|text]