gnu: Add freebayes.

* gnu/packages/bioinformatics.scm (freebayes): New variable.
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Pierre Neidhardt 2019-05-18 19:26:40 +02:00 committed by Efraim Flashner
parent 95fb1a1851
commit 8803dbdad8
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@ -15101,3 +15101,126 @@ 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 freebayes
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
(revision "1")
(version "1.0.2"))
(package
(name "freebayes")
(version (git-version version revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/freebayes.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
("htslib" ,htslib)))
(native-inputs
`(("bc" ,bc) ; Needed for running tests.
("samtools" ,samtools) ; Needed for running tests.
("parallel" ,parallel) ; Needed for running tests.
("perl" ,perl) ; Needed for running tests.
("procps" ,procps) ; Needed for running tests.
("python" ,python-2) ; Needed for running tests.
("bamtools" ,bamtools)
("vcflib-src" ,(package-source vcflib))
;; These are submodules for the vcflib version used in freebayes.
;; This package builds against the .o files so we need to extract the source.
("tabixpp-src" ,(package-source tabixpp-freebayes))
("smithwaterman-src" ,(package-source smithwaterman))
("multichoose-src" ,(package-source multichoose))
("fsom-src" ,(package-source fsom))
("filevercmp-src" ,(package-source filevercmp))
("fastahack-src" ,(package-source fastahack))
("intervaltree-src"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/intervaltree/")
(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
(file-name "intervaltree-src-checkout")
(sha256
(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
;; These submodules are needed to run the tests.
("bash-tap-src" ,(package-source bash-tap))
("test-simple-bash-src"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ingydotnet/test-simple-bash/")
(commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
(file-name "test-simple-bash-src-checkout")
(sha256
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
(arguments
`(#:tests? #f ; TODO: Re-enable when we have grep with perl support.
#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
(with-directory-excursion target
(if (file-is-directory? (assoc-ref inputs source))
(copy-recursively (assoc-ref inputs source) ".")
(invoke "tar" "xvf"
(assoc-ref inputs source)
"--strip-components=1"))))))
(and
(unpack "vcflib-src" "vcflib")
(unpack "fastahack-src" "vcflib/fastahack")
(unpack "filevercmp-src" "vcflib/filevercmp")
(unpack "fsom-src" "vcflib/fsom")
(unpack "intervaltree-src" "vcflib/intervaltree")
(unpack "multichoose-src" "vcflib/multichoose")
(unpack "smithwaterman-src" "vcflib/smithwaterman")
(unpack "tabixpp-src" "vcflib/tabixpp")
(unpack "test-simple-bash-src" "test/test-simple-bash")
(unpack "bash-tap-src" "test/bash-tap")))))
(add-after 'unpack-submodule-sources 'fix-makefile
(lambda* (#:key inputs #:allow-other-keys)
;; We don't have the .git folder to get the version tag from.
(substitute* '("vcflib/Makefile")
(("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version)))))
(replace 'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
(with-directory-excursion "vcflib"
(with-directory-excursion "tabixpp"
(pk "Compile tabixpp before compiling the main project.")
(let ((htslib-ref (assoc-ref inputs "htslib")))
(invoke "make" "HTS_HEADERS="
(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
(string-append "LIBPATH=-L. -L" htslib-ref "/include"))))
(pk "Compile vcflib before compiling the main project.")
(invoke "make" "CC=gcc"
(string-append "CFLAGS=\"" "-Itabixpp "
"-I" (assoc-ref inputs "htslib") "/include " "\"")
"all"))
(pk "Compile the main project.")
(with-directory-excursion "src"
(substitute* "Makefile"
(("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools"))
(invoke "make"
(string-append "BAMTOOLS_ROOT="
(assoc-ref inputs "bamtools"))))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "bin/freebayes" bin)
(install-file "bin/bamleftalign" bin))
#t)))))
(home-page "https://github.com/ekg/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))))