| Message ID | 171645804083.6.7508412953776945309.337355746@mawumag.com |
|---|---|
| State | New |
| Headers | show |
| Series | [bug#71146] gnu: kallisto: Update to 0.50.1 | expand |
Ricardo Wurmus <rekado@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?
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 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
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(-) 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