guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 209a8025f8f1f4d784b4cd21ca9ae60f73686944
Author: Andreas Enge <[email protected]>
AuthorDate: Mon Feb 23 17:38:24 2026 +0100
gnu: Remove freebayes.
* gnu/packages/bioinformatics.scm (freebayes): Delete variable.
Change-Id: I19fadd85a384cb4520160cfab04b114e5ca47cec
---
gnu/packages/bioinformatics.scm | 68 -----------------------------------------
1 file changed, 68 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad15af0af2..46472b0706 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22739,74 +22739,6 @@ format, and a collection of command-line utilities for
executing complex
manipulations on VCF files.")
(license license:expat)))
-(define-public freebayes
- (package
- (name "freebayes")
- (version "1.3.9")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/freebayes/freebayes";)
- (commit (string-append "v" version))
- (recursive? #true)))
- (file-name (git-file-name name version))
- (sha256
- (base32
"18i8xv5cx4n9924f4gqjk2sg3vi437nh7ssy99ng8ajschgaw1m2"))))
- (build-system meson-build-system)
- (inputs
- (list bzip2 fastahack htslib smithwaterman tabixpp vcflib xz))
- (native-inputs
- (list bc
- grep ; Built with perl support.
- parallel
- perl
- perl6-tap-harness
- pkg-config
- python
- samtools
- simde))
- (arguments
- (list
- #:phases
- `(modify-phases %standard-phases
- (add-after 'unpack 'patch-source
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "CPLUS_INCLUDE_PATH"
- (string-append (getcwd) "/contrib/multichoose:"
- (getenv "CPLUS_INCLUDE_PATH")))
- (substitute* '("src/BedReader.cpp"
- "src/BedReader.h")
- (("intervaltree/IntervalTree.h") "vcflib/IntervalTree.h")
- (("<IntervalTree.h>") "<vcflib/IntervalTree.h>"))
- (substitute* '("src/AlleleParser.h"
- "src/ResultData.h")
- (("Variant.h") "vcflib/Variant.h"))
- (substitute* (find-files "." "\\.(h|c)(pp)?$")
- (("\"multichoose.h\"") "<vcflib/multichoose.h>")
- (("\"convert.h\"") "<smithwaterman/convert.h>")
- (("\"split.h\"") "<fastahack/split.h>")
- (("\"join.h\"") "<vcflib/join.h>"))
- (substitute* "meson.build"
- ;; Our pkg-config file is vcflib.pc
- (("libvcflib") "vcflib")
- (("vcflib_inc,") ""))))
- ;; The slow tests take longer than the specified timeout.
- ,@(if (any (cute string=? <> (%current-system))
- '("armhf-linux" "aarch64-linux"))
- '((replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "meson" "test" "--timeout-multiplier" "5")))))
- '()))))
- (home-page "https://github.com/freebayes/freebayes";)
- (synopsis "Haplotype-based variant detector")
- (description "FreeBayes is a Bayesian genetic variant detector designed to
-find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
-indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
-complex events (composite insertion and substitution events) smaller than the
-length of a short-read sequencing alignment.")
- (license license:expat)))
-
(define-public samblaster
(package
(name "samblaster")
