Default program settings

As with many other areas, the default behaviour of programs can be controlled by setting appropriate values in

.embossrc

.

All general qualifiers^3.16 can be specified as

set emboss_QUALIFIER 1

where

QUALIFIER

is one of the general qualifiers and the value can be

1

or

1

for true, or

0

or

N

for false.

Setting the qualifier value to true has the effect of running every program with that qualifier set.^3.17 Qualifiers can be set and will work in the same way as if you set them when running the program. For example you can

set emboss_verbose
Y

and the program will run normally, but when the program is run with the

-help

qualifier, the output will be in verbose form.

There is no point in globally setting options that are there for producing help output.

Qualifiers that can be set:

VERBOSE

Causes

-help

to print verbose text.

STDOUT

Causes all output to go to

STDOUT

as default. Programs will usually build a default output file name form the input sequence and the program name.

DEBUG

Writes debugging output to a file. Useful for finding bugs as a command line option.

OPTIONS

Enable prompting for optional parameters.

FILTER

Take input from

STDIN

and send it to

STDOUT

, and turn on

-auto

AUTO

Do not prompt for any options but accept the defaults if no values are given.

WARNING

Print warning messages to

STDERR

(default is true)

ERROR

Print error messages to

STDERR

(default is true)

FATAL

Print fatal messages to

STDERR

(default is true)

DIE

Print crash messages to

STDERR

These general qualifiers are typically used by advanced users (

-options

,

-verbose

) or by developers (

-debug -acdlog

).

Other program options that can be set are

emboss_format

,

emboss_acdroot

, and

emboss_data

. The value of

emboss_format

determines which default sequence format to use for output. for example, if you are running EMBOSS alongside GCG you may wish to have the following entry in your .embossrc

set emboss_FORMAT gcg
set emboss_OUTFORMAT gcg

which has the effect of using GCG format by default.^3.18

emboss_acdroot

/path/to/acd

can be set if you wish to use a different directory for the ACD files, and

emboss_data

/path/to/data

if you wish to use a separate data directory.