[Debian-med-packaging] Fwd: Re: Please upload NEW hhsuite

[Andreas Hauser]

Am 24.02.2012 11:34, schrieb Laszlo Kajan:
> Hello Andreas!
>
>>> * Create symlinks so that /usr/lib/hh or /usr/lib/hh/data/context_data.lib remain valid, but install files where they more naturally fall
>>> according to the FHS or established practices, so install into /usr/lib/hhsuite arch-dep files (e.g. do_not_delete.p??) and install into
>>> /usr/share/hhsuite arch indep files (e.g. data/context_data.lib). Present paths then should remain valid.
>>
>> *If* there would be reasons to be afraid of incompatibilities for
>> different architectures for these binary files we definitely need
>> the source which is needed to create those files.  (It would be
>> good to have hte source anyway because ftpmaster might stumble
>> upon a "binary withouot source" issue.)
>
> Can you please tell me how those do_not_delete.p?? in /usr/lib/hh(suite)/data are generated? If it is in the manual, could you please just send
> me the section/page where to look? I haven't yet read that document... mea culpa!

They are generated from the do_not_delete_me (source!) fasta via formatdb:
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/blast/formatdb.html

I'm not sure about their portability. They are not used by the binary programs
in hhsuite and are only needed for some of the scripts that enhance on their output,
using e.g. psi-blast, which for some of those uses needs a dummy DB.
If Debian already includes some dummy DB for a similar use, that could probably
be used instead.

The other files are text data files and scripts and should be portable, afais.


Cheers
Andy
-- 
Andreas Hauser, Scientific Computing, ☎ +49 89 2180 76719
Gene Center Munich, Department of Biochemistry
Ludwig-Maximilians-Universität München (LMU)
Feodor-Lynen-Str. 25, 81377 München, Bayern