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new d190f22813 gnu: Remove khmer.
d190f22813 is described below
commit d190f22813458c595fbf002ee0af948295f9323c
Author: Andreas Enge <[email protected]>
AuthorDate: Mon Jan 5 17:11:11 2026 +0100
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 a702188bf4..d063c276e0 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")
