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;; To use this file to build HEAD of freebayes:
;;
;; guix build -f guix.scm
;;
;; To get a development container
;;
;; guix shell -C -D -F -f guix.scm
;;
;; For the tests you need /usr/bin/env. Inside the container:
;;
;; mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
;;
;; meson setup build/ --buildtype debug
;; cd build
;; ninja
;; ninja test
(use-modules
((guix licenses) #:prefix license:)
(guix gexp)
(guix packages)
(guix git-download)
(guix build-system meson)
(gnu packages algebra)
(gnu packages assembly)
(gnu packages base)
(gnu packages compression)
(gnu packages bioinformatics)
(gnu packages build-tools)
(gnu packages curl)
(gnu packages gcc)
(gnu packages gdb)
(gnu packages llvm)
(gnu packages ninja)
(gnu packages parallel)
(gnu packages perl)
(gnu packages perl6)
(gnu packages pkg-config)
(gnu packages python)
(srfi srfi-1)
(ice-9 popen)
(ice-9 rdelim))
(define %source-dir (dirname (current-filename)))
(define %git-commit
(read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
(define-public freebayes-git
(package
(name "freebayes-git")
(version (git-version "1.3.6" "HEAD" %git-commit))
(source (local-file %source-dir #:recursive? #t))
(build-system meson-build-system)
(propagated-inputs
`(
;; for the libs also see contrib/README.md
("bzip2-static" ,bzip2 "static") ; libz2 part of htslib for static builds
("fastahack" ,fastahack) ; shared lib used by vcflib; bundle for Debian
("grep" ,grep) ; for testing
("htslib" ,htslib) ; does work, but lacks codecs
("intervaltree" ,intervaltree)
("perl" ,perl) ; for testing
("python" ,python) ; for testing
("samtools" ,samtools) ; for testing
("simde" ,simde)
("smithwaterman" ,smithwaterman) ; vcflib shared lib dependency ; bundle for Debian
("tabixpp" ,tabixpp) ; for htslib
("vcflib" ,vcflib) ; for testing freebayes-parallel
("wfa2-lib" ,wfa2-lib) ; vcflib shared lib dependency
("which" ,which) ; for version
("xz-static" ,xz "static") ; for static builds
("zlib-static" ,zlib "static")))
(native-inputs
`(
("meson" ,meson)
("ninja" ,ninja)
("gdb" ,gdb)
("pkg-config" ,pkg-config)
))
(inputs
`(
;; ("clang" ,clang) ; add this to test clang builds
;; ("lld" ,lld) ; add this to test clang builds
;; ("gcc" ,gcc-13)
("bc" ,bc) ; for tests
("coreutils" ,coreutils) ; for echo and env in tests
("curl" ,curl)
("perl6-tap-harness" ,perl6-tap-harness) ; for tests
("parallel" ,parallel) ; for freebayes-parallel
("zlib" ,zlib)
("xz" ,xz) ; liblzma part of htslib
("bzip2" ,bzip2) ; libz2 part of htslib
))
(arguments
`(#:phases (modify-phases %standard-phases
;; add timeout extension for slower processors
(replace 'check
(lambda _
(invoke "meson" "test" "--timeout-multiplier" "5"))))))
(synopsis "freebayes haplotype-based genetic variant caller")
(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.")
(home-page "https://github.com/freebayes/freebayes")
(license license:expat)))
freebayes-git
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