Subject: [bug#71146] [PATCH] gnu: kallisto: Update to 0.50.1

From: Ricardo Wurmus <[email-masked]>
Date: Sat, 01 Jun 2024 21:13:10 +0200

Ricardo Wurmus <[email-masked]> writes:

>> I had to modify the 'do-not-use-bundled-htslib snippet to make one
>> regex more selective---in this new version it the previous regex was
>> mistakenly modifying parts of CMakeLists.txt other than the intended
>> one.
>
> It looks like this might not be working as intended.  I used:
>
>     guix gc -R $(./pre-inst-env guix build kallisto)
>
> and it shows me that the newly built kallisto does not link with our
> htslib.  Perhaps it used the static library?

Turns out it's not actually using htslib at all, because USE_BAM is not
set.  It uses a bundled copy of bifrost instead.  If we want to build
kallisto with bifrost only then we should remove htslib from the inputs,
package bifrost (https://github.com/pmelsted/bifrost) and unbundle it
from kallisto, linking with the shared library.

Does this sound like a good plan or should we use htslib instead?

-- 
Ricardo