NGCHM-initialization: Initialization of the NGCHM library.

In bmbroom/NGCHMR: Utilities for Creating Next Generation Clustered Heat Maps

Initialization of the NGCHM library.

Description

When first loaded the NGCHM library reads configuration files in the configuration path specified by the NGCHMCONFIGPATH environment variable. The configuration path is a colon (:) separated list of directory names. If not set it defaults to /etc/ngchm:/usr/local/ngchm:/opt/ngchm:$HOME/.ngchm.

Details

For each configuration directory in the configuration path, the NGCHM package reads the contents of the configuration files in the conf.d subdirectory in order (as determined by the R sort function). Other subdirectories are not scanned unless instructed to by an entry in a configuration file.

Configuration files may be either text files (.txt extension), R scripts (.R extension), or javascript files (.js extension).

Text files

A text configuration file consists of one or more sections. Each section begins with a single line containing the section type enclosed in square brackets. Subsequent lines in the section are either blank or contain a definition of the form "name separator value". The default separator is the equals sign (=).

The 'servers' section defines available servers. The name field defines the name by which the server is known to the library. The value field specifies a directory containing a specification of the server's properties. The server specification directory must contain a config.txt that contains lines of the form "name separator value". The config.txt file must define the value of 'serverProtocol' to be the name of a ngchmServerProtocol. It must also define the values of any mandatory parameters required by ngchmServerProtocol, and may optionally define any optional parameters.

R scripts

R scripts are sourced. They can be used to define local NGCHM related functions.

Javascript scripts

Javascript files define context specific menu entries.

Examples

## Not run: 
#/usr/local/ngchm/conf.d/00-servers.txt :
[servers]
my-server = /usr/local/ngchm/my-server

## End(Not run)
## Not run: 
#/usr/local/ngchm/my-server/config.txt :
serverProtocol = manual

## End(Not run)

bmbroom/NGCHMR documentation built on April 18, 2022, 6:52 p.m.