From: guix--- via Guix-patches via <guix-patches@gnu.org>
To: 71146@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: [bug#71146] [PATCH] gnu: kallisto: Update to 0.50.1
Date: Thu, 23 May 2024 09:53:54 +0000 [thread overview]
Message-ID: <171645804083.6.7508412953776945309.337355746@mawumag.com> (raw)
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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.
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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
next reply other threads:[~2024-05-23 13:38 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2024-05-23 9:53 guix--- via Guix-patches via [this message]
[not found] ` <87wmn8kcpa.fsf@elephly.net>
2024-06-01 19:13 ` [bug#71146] [PATCH] gnu: kallisto: Update to 0.50.1 Ricardo Wurmus
2024-06-04 15:36 ` guix--- via Guix-patches via
2024-06-01 19:13 ` Ricardo Wurmus
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