[Debian-med-packaging] tool names in codonw

[Sascha Steinbiss]

Dear John,

I'm contacting you on behalf of the Debian Med team, a group within the
Debian project that targets software for biology and medicine. I am currently packaging CodonW for Debian but we have noticed a slight problem with it that you might be able to help us with.

The issue is that the names of several symlinked 'tools' created by the installation do clash with the names of separate binaries from other software packages, e.g. CodonW's ‘cai' tool clashes with the EMBOSS executable of the same name. We are wondering whether probably a rename of the symlinked tools would be OK with you (and probably find its way into a new release of CodonW?). For example, a prefix of ‘codonw-‘ could do the trick.
We could just rename the problematic symlinks in Debian but we would definitely prefer a solution that we both are happy with.

Of course, if you have a different suggestion I would be happy to hear it.

FYI, these are the problematic symlinks and the packages they conflict with:

emboss: /usr/bin/cai
cu: /usr/bin/cu
fop: /usr/bin/fop
graphviz: /usr/bin/gc
tidy: /usr/bin/tidy

Please let me know what you think.

Many thanks in advance,
Sascha