Overview

OpenCGA is delivered with three different command lines (opencga.sh, opencga-admin.sh and opencga-analysis.sh). All of them follow the same structure that could be divided into three different sections (header, usage, and list of commands).

Header

The header always contains meta information regarding the program being runned, the current version, the git commit to be able to reproduce again the same results and a general description.

Program: OpenCGA (OpenCB)

Version: 1.0.0-rc3

Git commit: f42850ff3ff1acb8d0a1bac710c9ec38e084fee5

Description: Big Data platform for processing and analysing NGS data

Usage

The command lines always starts with the executable followed by the list of of commands and options.

Usage: opencga.sh [-h|--help] [--version] <command> [options]

Some of the common options for the three command lines are:

• -h, --help: This is used to see the help of the command line (header, usage and available commands). This option is also available with any command or subcommand. In those cases, the usage and the available options will be shown.

• --version: This parameter is used to show the version and the git commit such as in the header.

Commands

The available commands are shown in this section together with a brief description containing the aim of each one. In order to successfully run an OpenCGA command line, a proper command, subcommand and options have to be supplied.

A list containing the available subcommands will be shown when only a command is provided (./opencga.sh users will show the list of subcommands available such as create, info, update…).

A list containing all the different parameters (options) available for an action is offered when the command and the subcommand are successfully provided. Let’s imagine we run ./opencga.sh users create:

The following options are required: -p, --password -e, --email -n, --name -u, --user

Usage: opencga.sh users create [options]

Options:

-C, --conf STRING Configuration folder that contains opencga.yml, catalog-configuration.yaml, storage-configuration.yml and client-configuration.yaml files.

* -e, --email STRING User email

-h, --help Print this help [false]

--log-file STRING Set the file to write the log

-L, --log-level STRING One of the following: 'error', 'warn', 'info', 'debug', 'trace' [info]

-M, --metadata Include metadata information [false]

* -n, --name STRING User name

--no-header Not include headers in the output (not applicable to json output-format) [false]

-o, --organization STRING User organization

--of, --output-format STRING Output format. one of {JSON, JSON_PRETTY, TEXT, YAML} [TEXT]

* -p, --password STRING User password

--project-alias STRING Project alias: Default: default

--project-description STRING Project description.

--project-name STRING Project name. Default: Default

--project-organization STRING Project organization

-S, --sid, --session-id STRING Token session id

* -u, --user STRING User id, this must be unique in OpenCGA

-v, --verbose Increase the verbosity of logs [false]

The options are shown formatted in three columns:

• The first column shows the parameter that has to be written (generally with a short and long form). We have decided to use upper case for short forms that are generic and can be used in any command line. Options preceded by an asterisc (*) are mandatory parameters. This means that the command line will not run unless those parameters are provided. Other parameters are optional.

• The second columns shows the type of input expected for that option. Generally, it will be STRING when a string is expected after the parameter or empty when the option is a boolean, meaning that the option will be active if parameter is written.

• The third column shows a description of the parameter. In some of them we can find in brackets the default value if not written.

The options that are always available are:

• -C, --conf: If not defined, the command line will assume that the configuration folder can be found in the parent folder where the executable is found (../conf). If that is not the case or if the user wants to use other configuration files available in a different path, the path should be provided.

• -h, --help: Shows the help with the list of options. Generally this is not necessary because there is almost always a mandatory parameter to be provided, although it is needed in a few cases if user wants to see the options.

• --log-file: By default, all the logs generated by the command lines are printed in the screen. However, the user might want to redirect the logs to another file. For those cases, the user will need to provide the file where the logs will be stored.

• -L, --log-level: There are 5 different log levels. EXPLAIN THIS BETTER.

• -M, --metadata:

opencga.sh

opencga-admin.sh

opencga-analysis.sh

General information

Usage