EMBOSS: C2 Environment Variables
The startup files "emboss.default" and
"$HOME/.embossrc" can define environment variables
which the user can override using "setenv". These can
control many aspects of EMBOSS.
- List of sequence formats used by default for input. If GCG is
used, please make sure it appears before formats that could be found in
a GCG file (e.g. EMBL).
- Directory for the EMBOSS data files, defaults to the "data" directory
in the original distribution.
- Directory for the EMBOSS ACD files, defaults to the "emboss/acd"
directory in the original distribution.
- NUmber of times the user can be prompted before EMBOSS gives up.
Default value is 1.
- Sets the "-filter" command switch.
If set to "Yes", all applications read from stdin and write to stdout.
The user cannot be prompted, so implies EMBOSS_AUTO.
- Sets the "-stdout" command switch.
If set to "Yes", all applications read from stdin and write to stdout
- Sets the "-auto" command switch.
If set to "Yes", all applications must have everything specified on
the command line.
- Sets the "-debug" command switch.
If set to "Yes", all applications write ".dbg" debug output files.
- Sets the "-options" command switch.
If set to "Yes", the user is prompted for "required" and "optional"
- Directories are defined simply by environment variables. These
could be extended to lists of directories just like VMS searchlists,
which would be useful for data file locations and for alternative ACD
file directories. If so, there must be general routines which
understand these and open files in the first directory where the
- What other variables would be useful?
- The prefix "emboss_" is assumed in all variables, but should be specified
in the emboss.default and .embossrc files.
- Variables can include other variables using the syntax
"$varname". This is useful for directory names etc. Remember that
such a variable can be replaced by the user's own setenv