GNU bug report logs - #71146
[PATCH] gnu: kallisto: Update to 0.50.1

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: guix <at> mawumag.com
To: guix-patches <at> gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH] gnu: kallisto: Update to 0.50.1
Date: Thu, 23 May 2024 09:53:54 +0000

[Message part 1 (text/plain, inline)]

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.

[0001-gnu-kallisto-Update-to-0.50.1.patch (text/x-patch, attachment)]

Message #8 received at 71146 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: guix <at> mawumag.com
Cc: 71146 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: kallisto: Update to 0.50.1
Date: Sat, 01 Jun 2024 21:13:10 +0200

Ricardo Wurmus <rekado <at> elephly.net> 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

Message #11 received at 71146 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: guix <at> mawumag.com
Cc: 71146 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: kallisto: Update to 0.50.1
Date: Sat, 01 Jun 2024 21:13:30 +0200

Thank you for the patch!

> 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?

-- 
Ricardo

Message #14 received at 71146 <at> debbugs.gnu.org (full text, mbox):

From: guix <at> mawumag.com
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 71146 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: kallisto: Update to 0.50.1
Date: Tue, 04 Jun 2024 15:36:41 +0000

> Ricardo Wurmus rekado <at> 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?

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

Message #19 received at 71146-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 71146-done <at> debbugs.gnu.org
Cc: guix <at> mawumag.com
Subject: [PATCH] gnu: kallisto: Update to 0.50.1
Date: Mon, 04 Nov 2024 15:51:22 +0100

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

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