Re: [PATCH] gnu: Add mash.

[Marius Bakke <mbakke@fastmail.com>]

Leo Famulari <leo@famulari.name> writes:

>> +         (add-after 'unpack 'fix-includes
>> +           (lambda _
>> +             (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
>> +               (("^#include \"kseq\\.h\"")
>> +                "#include \"htslib/kseq.h\""))
>> +             #t))
>> +         (add-before 'configure 'autoconf
>> +           (lambda _ (zero? (system* "autoconf")))))))
>> +    (native-inputs
>> +     `(("autoconf" ,autoconf)
>> +       ("capnproto" ,capnproto)
>> +       ("htslib" ,htslib)))
>
> Does it only need to use capnproto and htslib while building? Okay if
> so.

I had these in inputs initially and was surprised to see no references.
Both seems to be compiled into the final program[0]: when running "mash
info" on an invalid file (the provided data/refseq.msh), a generic
capnproto exception is thrown (src/capnp/serialize.c++:159).

That raises another question: should the htslib and capnproto licenses
be listed too, since they are part of the binary output?

I'm not a bioinformatician (just a mere sysadmin for such), but have
been going through the tutorial and things appear to work fine.

0: https://github.com/marbl/Mash/blob/master/Makefile.in#L38