gnu: Add freebayes.
* gnu/packages/bioinformatics.scm (freebayes): New variable.master
Pierre Neidhardt
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
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format, and a collection of command-line utilities for executing complex
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manipulations on VCF files.")
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(license license:expat))))
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(define-public freebayes
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(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
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(revision "1")
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(version "1.0.2"))
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(package
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(name "freebayes")
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(version (git-version version revision commit))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/freebayes.git")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
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(build-system gnu-build-system)
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(inputs
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`(("zlib" ,zlib)
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("htslib" ,htslib)))
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(native-inputs
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`(("bc" ,bc) ; Needed for running tests.
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("samtools" ,samtools) ; Needed for running tests.
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("parallel" ,parallel) ; Needed for running tests.
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("perl" ,perl) ; Needed for running tests.
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("procps" ,procps) ; Needed for running tests.
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("python" ,python-2) ; Needed for running tests.
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("bamtools" ,bamtools)
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("vcflib-src" ,(package-source vcflib))
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;; These are submodules for the vcflib version used in freebayes.
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;; This package builds against the .o files so we need to extract the source.
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("tabixpp-src" ,(package-source tabixpp-freebayes))
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("smithwaterman-src" ,(package-source smithwaterman))
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("multichoose-src" ,(package-source multichoose))
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("fsom-src" ,(package-source fsom))
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("filevercmp-src" ,(package-source filevercmp))
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("fastahack-src" ,(package-source fastahack))
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("intervaltree-src"
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,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/intervaltree/")
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(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
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(file-name "intervaltree-src-checkout")
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(sha256
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(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
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;; These submodules are needed to run the tests.
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("bash-tap-src" ,(package-source bash-tap))
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("test-simple-bash-src"
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,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ingydotnet/test-simple-bash/")
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(commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
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(file-name "test-simple-bash-src-checkout")
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(sha256
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(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
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(arguments
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`(#:tests? #f ; TODO: Re-enable when we have grep with perl support.
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#:test-target "test"
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-after 'unpack 'unpack-submodule-sources
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((unpack (lambda (source target)
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(with-directory-excursion target
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(if (file-is-directory? (assoc-ref inputs source))
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(copy-recursively (assoc-ref inputs source) ".")
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(invoke "tar" "xvf"
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(assoc-ref inputs source)
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"--strip-components=1"))))))
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(and
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(unpack "vcflib-src" "vcflib")
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(unpack "fastahack-src" "vcflib/fastahack")
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(unpack "filevercmp-src" "vcflib/filevercmp")
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(unpack "fsom-src" "vcflib/fsom")
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(unpack "intervaltree-src" "vcflib/intervaltree")
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(unpack "multichoose-src" "vcflib/multichoose")
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(unpack "smithwaterman-src" "vcflib/smithwaterman")
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(unpack "tabixpp-src" "vcflib/tabixpp")
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(unpack "test-simple-bash-src" "test/test-simple-bash")
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(unpack "bash-tap-src" "test/bash-tap")))))
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(add-after 'unpack-submodule-sources 'fix-makefile
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(lambda* (#:key inputs #:allow-other-keys)
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;; We don't have the .git folder to get the version tag from.
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(substitute* '("vcflib/Makefile")
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(("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version)))))
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(replace 'build
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(lambda* (#:key inputs make-flags #:allow-other-keys)
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(with-directory-excursion "vcflib"
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(with-directory-excursion "tabixpp"
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(pk "Compile tabixpp before compiling the main project.")
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(let ((htslib-ref (assoc-ref inputs "htslib")))
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(invoke "make" "HTS_HEADERS="
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(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
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(string-append "LIBPATH=-L. -L" htslib-ref "/include"))))
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(pk "Compile vcflib before compiling the main project.")
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(invoke "make" "CC=gcc"
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(string-append "CFLAGS=\"" "-Itabixpp "
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"-I" (assoc-ref inputs "htslib") "/include " "\"")
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"all"))
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(pk "Compile the main project.")
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(with-directory-excursion "src"
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(substitute* "Makefile"
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(("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools"))
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(invoke "make"
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(string-append "BAMTOOLS_ROOT="
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(assoc-ref inputs "bamtools"))))))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
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(install-file "bin/freebayes" bin)
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(install-file "bin/bamleftalign" bin))
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#t)))))
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(home-page "https://github.com/ekg/freebayes")
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(synopsis "Haplotype-based variant detector")
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(description "FreeBayes is a Bayesian genetic variant detector designed to
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find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
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indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
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complex events (composite insertion and substitution events) smaller than the
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length of a short-read sequencing alignment.")
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(license license:expat))))
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