[PATCH] gnu: kallisto: Update to 0.50.1

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2 participants
  • guix
  • Ricardo Wurmus
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guix
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G
G
guix wrote on 23 May 11:53 +0200
(address . guix-patches@gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
171645804083.6.7508412953776945309.337355746@mawumag.com
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.
From 9bec1c5bf14b644ef7147b1bc66acaea6a903830 Mon Sep 17 00:00:00 2001
Message-ID: <9bec1c5bf14b644ef7147b1bc66acaea6a903830.1716457241.git.guix@mawumag.com>
From: Marco Baggio <guix@mawumag.com>
Date: Thu, 23 May 2024 08:52:06 +0200
Subject: [PATCH] gnu: kallisto: Update to 0.50.1

Change-Id: I1b048be328f6d1d5034dfe29688a44f2af0b026a
---
gnu/packages/bioinformatics.scm | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)

Toggle diff (48 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b7e8e54de2..8dee300320 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14820,7 +14820,7 @@ (define-public segemehl
(define-public kallisto
(package
(name "kallisto")
- (version "0.48.0")
+ (version "0.50.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -14829,7 +14829,7 @@ (define-public kallisto
(file-name (git-file-name name version))
(sha256
(base32
- "0wx1ndmhndsd60952piaa925lk8bjr59d2yr1m2hcsqcb6cdjwpn"))
+ "0zfs79mv75599cf9d7d3c5a3s8idgz9qvl4qfzhvhbd87y3dv7p0"))
(modules '((guix build utils)))
(snippet
'(delete-file-recursively "ext/htslib/"))))
@@ -14841,16 +14841,16 @@ (define-public kallisto
(add-after 'unpack 'do-not-use-bundled-htslib
(lambda _
(substitute* "CMakeLists.txt"
- (("^ExternalProject_Add" m)
+ (("^ExternalProject_Add\\(htslib[^\\)]*\\)" m)
(string-append "if (NEVER)\n" m))
- (("^\\)")
- (string-append ")\nendif(NEVER)"))
(("include_directories\\(\\$\\{htslib_PREFIX.*" m)
(string-append "# " m)))
(substitute* "src/CMakeLists.txt"
(("target_link_libraries\\(kallisto kallisto_core pthread \
-\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)")
- "target_link_libraries(kallisto kallisto_core pthread hts)")
+\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a \
+\\$\\{install_dir\\}/build/src/libbifrost.a\\)")
+ "target_link_libraries(kallisto kallisto_core pthread hts \
+${install_dir}/build/src/libbifrost.a)")
(("include_directories\\(\\.\\./ext/htslib\\)") "")))))))
(inputs
(list hdf5 htslib-1.9 zlib))

base-commit: 3597c736588c45efde3c22d533ea8774c3fdd235
--
2.41.0
R
R
Ricardo Wurmus wrote on 1 Jun 21:13 +0200
(address . guix@mawumag.com)(address . 71146@debbugs.gnu.org)
87le3ojx2x.fsf@elephly.net
Ricardo Wurmus <rekado@elephly.net> writes:

Toggle quote (12 lines)
>> 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
R
R
Ricardo Wurmus wrote on 1 Jun 21:13 +0200
(address . guix@mawumag.com)(address . 71146@debbugs.gnu.org)
87jzj8jx2d.fsf@elephly.net
Thank you for the patch!

Toggle quote (5 lines)
> 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
G
G
guix wrote on 4 Jun 17:36 +0200
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 71146@debbugs.gnu.org)
171751540946.7.6431104630771377265.346935814@mawumag.com
Toggle quote (10 lines)
> 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?

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
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