[Debian-med-packaging] Bug#879619: Autopkgtest for ncbi-tools6

[Aaron M. Ucko]

Liubov Chuprikova <chuprikovalv at gmail.com> writes:

> Sorry for a delay, but I was planning to make one more effort on extending
> the set of tests.

No problem.

> At the moment, the following commands are still lacking tests:
>
>    - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are
>    obsolete and/or unsupported)

- asn2ff plays the same general role as asn2flat, and should be possible to
  test similarly.
- gbseqget is like insdseqget, but formally uses GenBank-specific
  notation; as such, it requires network access.
- findspl also requires network access, and will need to be patched in the
  same fashion as taxblast; I'll take care of it when I get a chance.

>    - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they
>    require)

- I'm not sure where you'd find input for asndhuff.
- nps2gps takes a text Bioseq-set or Seq-entry of class nuc-prot, as
  obtained by (for instance) idfetch -g1234.

>    - *fa2htgs*, *spidey* (they look too complicated for me and require much
>    time to understand how they work)

That's fair.  You can always come back to them later if you feel inspired.

>    - *taxblast* doesn't generate an output file and only generates an
>    *incomplete* html

I'm not sure what's up with that, but as previously noted, it requires
network access anyway.

>    - *errhdr*, *sortbyquote* (I can't figure out even what they are
>    supposed to do)

- errhdr is a developer tool, working with files of the format found in
  errmsg/.
- sortbyquote is also a developer tool, essentially a variant of sort
  that ignores everything outside quotation marks (and generally has far
  fewer options).

> If nothing critical is left without a test, then I'd like to ask you to
> sponsor the upload. If you need any additional information about *taxblast*,
> I'll be happy to provide it.

OK, thanks.  I'm not sure any of these is critical to test, but some
should be relatively straightforward to work in at this point, and as
noted I'm not quite ready to upload a new version anyway.

-- 
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