[Biopython-dev] 1.62b test coverage report

[Peter Cock]

On Fri, Aug 2, 2013 at 10:31 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> The NCBI_BLAST error involves rpsblast not being in the install.
>> Version 2.2.25-7 using apt-get.
>
> I believe this is down to an NCBI stupidity with binary name
> clashes, both the old 'legacy' C BLAST and the new C++
> BLAST+ suite have a binary called rpsblast.
>
> Our test code copes with this by searching the path and checking
> each rpsblast binary found - looking for the new version only.
>
> However, Debian policy is to resolve ambiguities like this with
> a unilateral renaming - in this case I *think* they called the new
> binary rpsblast+ instead. Can you confirm that? I don't have
> access to a Debian machine right now.

Certainly this was their plan and was done on Bio-Linux,
http://lists.debian.org/debian-med/2011/05/msg00025.html

> So, strictly speaking the Biopython test is correct - you don't
> have the new rpsblast installed. However, it would be more
> helpful if we also checked for the Debian alias rpsblast+ too.
>
> That shouldn't be too complicated to do - especially if you
> could rerun the tests using Biopython from git for me?

This commit is now on our master branch,

https://github.com/biopython/biopython/commit/148b681a66061cc03d70f940a2efdede29adc64a

Thanks,

Peter