[Debian-med-packaging] Bug#848394: metastudent-data: FTBFS: Error: Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''

[Aaron M. Ucko]

olivier sallou <olivier.sallou at gmail.com> writes:

>> I guess that's due to the new version of ncbi-tools+.  Any suggested
>> patch for this problem?
>>
> By the way, adding dbtype with prot or nuc value should do the job.
> If dataset_201401/MFO/goasp.fasta contains only acgtn chars it is nuc
> If it contains other letters it is prot

The input files definitely look like protein data, as confirmed by the
output filenames (*.fasta.p??).  However, metastudent-data's makefile
can't pass -dbtype prot directly unless it starts running makeblastdb
directly; as it is, it should add "-p".  (FTR, for nucleotides, the
option would be "-p F".)

An equivalent makeblastdb command line would take the form

  makeblastdb -in .../goasp.fasta -dbtype prot -out .../goasp.fasta

I would also recommend updating metastudent-data's build dependency on
blast2 to either

  ncbi-blast+

or

  ncbi-blast+-legacy (>= 2.5) | blast2

depending on whether it winds up running makeblastdb directly or via
formatdb.

-- 
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