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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[*] can be specified as


set emboss_QUALIFIER 1
where QUALIFIER is one of the general qualifiers and the value can be 1 or 0 for true or false respectively. Setting the qualifier value to true has the effect of running every program with that qualifier set.[*] multiple 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 1 and the program will run normally, but when the program is run with the -help qualifier, the output will be in verbose form.

Qualifiers that can be set:

HELP
Print help text.
VERBOSE
Causes -help to print verbose text.
ACDTABLE
Causes -help to print HTML formatted table of options.
STDOUT
Causes all output to go to STDOUT as default.
ACDPRETTY
Rewrites the ACD file in a nicely formatted way.
ACDLOG
Enables ACD file processing to be logged. Useful for hunting bugs.
DEBUG
Writes debugging output to a file. Also useful for finding bugs.
OPTIONS
Enable prompting for optional parameters.
FILTER
Take input from STDIN and send it to STDOUT.
AUTO
Do not prompt for any options but accept the defaults if no values are given.

These 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
which has the effect of using GCG format by default.[*]

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.


next up previous contents
Next: Logging Up: Configuration Previous: Miscellaneous data files
EMBnet Manager
8/17/2000