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 1where 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.
Qualifiers that can be set:
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 gcgwhich 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.