Configuration

EMBOSS can be readily configured to match your requirements. In a standard installation of EMBOSS the configuration directives are looked for in the following locations and in the following search order:

1. A file

   emboss.default

   in the

   share/EMBOSS

   subdirectory of your EMBOSS installation.^3.13.2
2. A file

   .embossrc

   in the directory specified by the

   EMBOSSRC

   environment variable.
3. A file

   .embossrc

   in the users home directory.

emboss.default

and

.embossrc

are plain text files that can readily be edited to suit.^3.3 Redefinitions of configuration parameters will override those previously defined. In the descriptions that follow only

.embossrc

will be mentioned but all directives can be placed in

emboss.default

for site wide configuration.

Several aspects of EMBOSS can be defined. These are:

• EMBOSS environment variables
• EMBOSS databases
• Default behaviour of EMBOSS programs

Databases are by far the most complex of these.

EMBOSS will ignore blank lines in the

emboss.default

and

.embossrc

files. It will also ignore any lines beginning with

#

or

!

allowing comments to illuminate the declarations in the file.