[PATCH] gnu: kallisto: Update to 0.50.1

Updated kallisto to 0.50.1, it now supports more single-cell technologies (e.g. SPLiT-seq).

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.

Ricardo Wurmus <rekado@elephly.net> writes:

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

Thank you for the patch!

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?

--

Ricardo

My initial attempt was to unbundle bifrost from kallisto, but I had two concerns:

- I was not able to determine the exact version of bifrost that was bundled with kallisto (it is definitely not the latest one, as the relevant ext/bifrost directory in kallisto is older).

This is also a problem with htslib, I am sure whoever packaged kallisto 0.48.0 was careful to choose the correct version, but I would not know how to verify this.

This has the potential to lead to mismatches (or even bugs) between the guix version and the official one compiled from their sources.

- Some header files of bifrost appear to be included in kallisto source code directly, but it was not clear to me how to include bifrost in guix in a way that exports its libraries and headers.

Especially for the first reason, I would actually propose to use the bundled htslib and bifrost for kallisto. Both are bundled as source code and are compiled during the build process, so this should not pose a concern (bifrost is released under BSD 2-Clause License, like kallisto, while htslib is released under expat).

Please let me know what you think.

Cheers,

Marco

Hi,

I'm back to work now and just reviewed our discussion on kallisto.

We

may want to revisit the decision to not unbundle libbifrost and

htslib

at a later point, but at the moment I agree to keep the bundled

libraries until we've attained more clarity.

I removed the now obsolete build phase completely and I disabled

parallel building (see comment).

Thanks for the patch and my apologies for not being able to merge

this

sooner!

--

Ricardo