From d190f22813458c595fbf002ee0af948295f9323c Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Mon, 5 Jan 2026 17:11:11 +0100
Subject: [PATCH] gnu: Remove khmer.

* gnu/packages/bioinformatics.scm (khmer): Delete variable.

Fixes: guix/guix#4489
Change-Id: I88aca5be768690b236343f2e959ecb71b4a5c984
---
 gnu/packages/bioinformatics.scm | 80 ---------------------------------
 1 file changed, 80 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a702188bf4565ab68c2d650d383822456af1709c..d063c276e012c100407a1a032e9eaed52a3ff38a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9742,86 +9742,6 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
     ;; One of these licenses may be picked
     (license (list license:gpl3+ license:bsd-3))))
 
-(define-public khmer
-  (package
-    (name "khmer")
-    (version "3.0.0a3")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/dib-lab/khmer")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "01l4jczglkl7yfhgvzx8j0df7k54bk1r8sli9ll16i1mis0d8f37"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Delete bundled libraries.  We do not replace the bundled seqan
-           ;; as it is a modified subset of the old version 1.4.1.
-           ;;
-           ;; We do not replace the bundled MurmurHash as the canonical
-           ;; repository for this code 'SMHasher' is unsuitable for providing
-           ;; a library.  See
-           ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
-           (delete-file-recursively "third-party/zlib")
-           (delete-file-recursively "third-party/bzip2")
-           (delete-file-recursively "third-party/seqan")
-           (substitute* "setup.cfg"
-             (("# libraries = z,bz2")
-              "libraries = z,bz2")
-             (("include:third-party/zlib:third-party/bzip2")
-              "include:"))
-           ;; Delete generated Cython CPP files.
-           (for-each delete-file (find-files "khmer/_oxli/" "\\.cpp$"))))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'set-cc
-           (lambda _ (setenv "CC" "gcc")))
-         (add-after 'unpack 'python-3.8-compatibility
-           (lambda _
-             ;; Python 3.8 removed time.clock().
-             (substitute* "sandbox/sweep-reads.py"
-               (("time\\.clock")
-                "time.process_time"))))
-         (add-after 'unpack 'do-use-cython
-           (lambda _
-             (substitute* "setup.py"
-               (("from setuptools import Extension as CyExtension")
-                "from Cython.Distutils import Extension as CyExtension")
-               (("from setuptools.command.build_ext import build_ext as _build_ext")
-                "from Cython.Distutils import build_ext as _build_ext")
-               (("HAS_CYTHON = False") "HAS_CYTHON = True")
-               (("cy_ext = 'cpp'") "cy_ext = 'pyx'"))))
-         (add-before 'build 'build-extensions
-           (lambda _
-             ;; Cython extensions have to be built before running the tests.
-             (invoke "python" "setup.py" "build_ext" "--inplace")))
-         (replace 'check
-           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "pytest" "-v")))))))
-    (native-inputs
-     (list python-cython python-pytest python-pytest-runner))
-    (inputs
-     (list zlib bzip2 seqan-1 python-screed python-bz2file))
-    (home-page "https://khmer.readthedocs.org/")
-    (synopsis "K-mer counting, filtering and graph traversal library")
-    (description "The khmer software is a set of command-line tools for
-working with DNA shotgun sequencing data from genomes, transcriptomes,
-metagenomes and single cells.  Khmer can make de novo assemblies faster, and
-sometimes better.  Khmer can also identify and fix problems with shotgun
-data.")
-    ;; When building on i686, armhf and mips64el, we get the following error:
-    ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
-    (supported-systems '("x86_64-linux" "aarch64-linux"))
-    (license license:bsd-3)))
-
 (define-public kaiju
   (package
     (name "kaiju")