EMBOSS: C2 Environment Variables

The startup files "emboss.default" and "$HOME/.embossrc" can define environment variables which the user can override using "setenv". These can control many aspects of EMBOSS.

Current List

EMBOSS_FORMAT

List of sequence formats used by default for input. If GCG is used, please make sure it appears before formats that could be found in a GCG file (e.g. EMBL).

EMBOSS_DATA

Directory for the EMBOSS data files, defaults to the "data" directory in the original distribution.

EMBOSS_ACDROOT

Directory for the EMBOSS ACD files, defaults to the "emboss/acd" directory in the original distribution.

EMBOSS_ACDPROMPT

NUmber of times the user can be prompted before EMBOSS gives up. Default value is 1.

EMBOSS_FILTER

Sets the "-filter" command switch. If set to "Yes", all applications read from stdin and write to stdout. The user cannot be prompted, so implies EMBOSS_AUTO.

EMBOSS_STDOUT

Sets the "-stdout" command switch. If set to "Yes", all applications read from stdin and write to stdout

EMBOSS_AUTO

Sets the "-auto" command switch. If set to "Yes", all applications must have everything specified on the command line.

EMBOSS_DEBUG

Sets the "-debug" command switch. If set to "Yes", all applications write ".dbg" debug output files.

EMBOSS_OPTIONS

Sets the "-options" command switch. If set to "Yes", the user is prompted for "required" and "optional" values.

Issues:

1. Directories are defined simply by environment variables. These could be extended to lists of directories just like VMS searchlists, which would be useful for data file locations and for alternative ACD file directories. If so, there must be general routines which understand these and open files in the first directory where the filename appears.
2. What other variables would be useful?
3. The prefix "emboss_" is assumed in all variables, but should be specified in the emboss.default and .embossrc files.
4. Variables can include other variables using the syntax "$varname". This is useful for directory names etc. Remember that such a variable can be replaced by the user's own setenv definition.