EMBOSS environment variables

EMBOSS environment variables are set with an '

env

' or a '

set

' declaration. '

env

' and '

set

' are interchangeable. The most important environment variable is the location of the

.acd

files that describe each program.

set emboss_acdroot /site/prog/emboss/share/EMBOSS/acd

Environment variables are useful for simplifying maintenance of your

.embossrc

. For example you may want to specify the location of your databases as an environment variable. Then if you move the databases you only have to update one line in the configuration file.

set emboss_database_dir /data/databases/flatfiles

This would then be referred to later in

.embossrc

as

\$emboss_database_dir/embl

for the directory

/data/databases/flatfiles/embl