EMBOSS: C2 Local Data Files

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

• . (your current directory)
• .embossdata (under your current directory)
• ~/ (your home directory)
• ~/.embossdata

Issues:

1. New local data files needed
2. File naming: do we need extensions for BLOSUM62, e.g. for non-Unix systems.
3. Search path for local data files
4. Utilities for local data file management