Re: [Help] Re: metastudent-data breaks metastudent autopkgtest: 255

[ucko@debian.org (Aaron M. Ucko)]

Control: tags -1 + upstream

Andreas Tille <andreas@an3as.eu> writes:

> Aaron (or whoever might want to check), do you have any idea?

Due to metastudent-data's unwieldiness, I haven't tested thoroughly, but
AFAICT the immediate, and with any luck only, problem is more fallout
from the switch to BLASTDB version 5 format by default, which we can
address in one of two ways:

- Patch metastudent-data's build system to include more generated output
  in install-data-local.  It should at minimum allow *.pdb in addition
  to *.phr, *.pin, and *.psq.  Additionally allowing *.pot, *.ptf, and
  *.pto would cover the full range of current BLAST database components
  (though the files with those three extensions appear to be relatively
  specialized and perhaps not strictly necessary), and allowing all of
  *.p?? would make for best futureproofing.

OR

- Patch the build system to produce a legacy V4 database, which would
  ironically require cutting out the legacy formatdb wrapper, by
  changing the formatdb invocation to

  makeblastdb -dbtype prot -in "$<" -out "$(@:.psq=)" -blastb_version 4

Thanks for checking!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu