guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 1a9576ab2150e789d3f7191dd8435eed8102964a
Author: Andreas Enge <[email protected]>
AuthorDate: Mon Feb 23 17:39:07 2026 +0100
gnu: Remove vcflib.
* gnu/packages/bioinformatics.scm (vcflib): Delete variable.
Change-Id: I3ffdcfdbd8a3bb9d573fc0d5dc03da59acdd482e
---
gnu/packages/bioinformatics.scm | 132 ----------------------------------------
1 file changed, 132 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46472b0706..3e3b4a9cf4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22607,138 +22607,6 @@ sequences to accelerate the alignment process.")
(properties `((tunable? . #t)))
(license license:expat)))
-(define-public vcflib
- (package
- (name "vcflib")
- (version "1.0.12")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/vcflib/vcflib";)
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1llqnbgx4ybb77cp5k3cs0y7n4p8ma6b3sj10iarpg5r6a5gps5a"))
- (modules '((guix build utils)))
- (snippet
- #~(begin
- (substitute* "CMakeLists.txt"
- ((".*fastahack.*") "")
- ((".*smithwaterman.*") "")
- (("(pkg_check_modules\\(TABIXPP)" text)
- (string-append
- "pkg_check_modules(WFA2 REQUIRED libwfa2)\n"
- "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
- "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
- text))
- (("\\$\\{TABIXPP_LIBRARIES\\}" text)
- (string-append "${FASTAHACK_LIBRARIES} "
- "${WFA2_LIBRARIES} "
- "${SMITHWATERMAN_LIBRARIES} "
- text))
- (("install\\(TARGETS \\$\\{WFALIB\\}.*") ""))
- (substitute* (find-files "." "\\.(h|c)(pp)?$")
- (("SmithWatermanGotoh.h") "smithwaterman/SmithWatermanGotoh.h")
- (("\"convert.h\"") "<smithwaterman/convert.h>")
- (("\"disorder.h\"") "<smithwaterman/disorder.h>")
- (("\"wavefront/wfa.hpp\"") "<wavefront/wfa.hpp>")
- (("Fasta.h") "fastahack/Fasta.h"))))))
- (build-system cmake-build-system)
- (inputs
- (list bzip2
- curl
- htslib
- fastahack
- perl
- python
- pybind11
- smithwaterman
- tabixpp
- xz
- zlib))
- (propagated-inputs
- (list wfa2-lib))
- (native-inputs
- `(("pkg-config" ,pkg-config)
- ;; Submodules.
- ;; This package builds against the .o files so we need to extract the
source.
- ("filevercmp-src" ,(package-source filevercmp))
- ("fsom-src" ,(package-source fsom))
- ("intervaltree-src" ,(package-source intervaltree))))
- (arguments
- (list
- #:configure-flags
- #~(list "-DZIG=OFF"
- "-DTABIXPP_LOCAL=OFF"
- "-DTABIX_FOUND=ON"
- "-DWFA_GITMODULE=OFF")
- #:tests? #f ; no tests
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'find-wfa2lib-headers
- (lambda _
- (setenv "CPLUS_INCLUDE_PATH"
- (string-append
- #$(this-package-input "wfa2-lib")
- "/include/wfa2lib:"
- (or (getenv "CPLUS_INCLUDE_PATH") "")))))
- (add-after 'unpack 'build-shared-library
- (lambda _
- (substitute* "CMakeLists.txt"
- (("vcflib STATIC") "vcflib SHARED"))))
- (add-after 'unpack 'unpack-submodule-sources
- (lambda* (#:key inputs native-inputs #:allow-other-keys)
- (let ((unpack (lambda (source target)
- (mkdir-p target)
- (with-directory-excursion target
- (let ((source (or (assoc-ref inputs source)
- (assoc-ref native-inputs
source))))
- (if (file-is-directory? source)
- (copy-recursively source ".")
- (invoke "tar" "xvf"
- source
- "--strip-components=1")))))))
- (and
- (unpack "filevercmp-src" "contrib/filevercmp")
- (unpack "fsom-src" "contrib/fsom")
- (unpack "intervaltree-src" "contrib/intervaltree"))
-
- ;; This is needed for downstream packages to allow building
- ;; with GCC 11+.
- (substitute* "contrib/intervaltree/IntervalTree.h"
- (("#include <vector>" m)
- (string-append m "
-#include <limits> /* std::numeric_limits */"))))))
- ;; This pkg-config file is provided by other distributions.
- (add-after 'install 'install-pkg-config-file
- (lambda _
- (let ((pkgconfig (string-append #$output "/lib/pkgconfig")))
- (mkdir-p pkgconfig)
- (with-output-to-file (string-append pkgconfig "/vcflib.pc")
- (lambda _
- (format #t "\
-prefix=~a~@
-exec_prefix=${prefix}~@
-libdir=${exec_prefix}/lib~@
-includedir=${prefix}/include~@
-~@
-Name: vcflib~@
-Version: ~a~@
-Requires: libwfa2, smithwaterman, fastahack, tabixpp~@
-Description: C++ library for parsing and manipulating VCF files~@
-Libs: -L${libdir} -lvcflib~@
-Cflags: -I${includedir}~%"
- #$output #$version)))))))))
- (home-page "https://github.com/vcflib/vcflib/";)
- (synopsis "Library for parsing and manipulating VCF files")
- (description "Vcflib provides methods to manipulate and interpret
-sequence variation as it can be described by VCF. It is both an API for
parsing
-and operating on records of genomic variation as it can be described by the VCF
-format, and a collection of command-line utilities for executing complex
-manipulations on VCF files.")
- (license license:expat)))
-
(define-public samblaster
(package
(name "samblaster")
