Subject: [PATCH] gnu: kallisto: Update to 0.50.1
From: [email-masked]
To: [email-masked]
Cc: Ricardo Wurmus <[email-masked]>
Date: Thu, 23 May 2024 09:53:54 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

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: <[email-masked]>
From: Marco Baggio <[email-masked]>
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