gnu: vcflib: Use G-expressions.
* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using G-expressions. [arguments]: Do not return #t from custom phases. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>master
Arun Isaac
Efraim Flashner
parent
9258576eea
commit
9a68c07507
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@ -14567,27 +14567,27 @@ library automatically handles index file generation and use.")
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(base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(substitute* "CMakeLists.txt"
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((".*fastahack.*") "")
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((".*smithwaterman.*") "")
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(("(pkg_check_modules\\(TABIXPP)" text)
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(string-append
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#~(begin
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(substitute* "CMakeLists.txt"
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((".*fastahack.*") "")
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((".*smithwaterman.*") "")
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(("(pkg_check_modules\\(TABIXPP)" text)
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(string-append
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"pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
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"pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
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text))
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(("\\$\\{TABIXPP_LIBRARIES\\}" text)
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(string-append "${FASTAHACK_LIBRARIES} "
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"${SMITHWATERMAN_LIBRARIES} "
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text)))
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(substitute* (find-files "." "\\.(h|c)(pp)?$")
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(("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
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(("\"convert.h\"") "<smithwaterman/convert.h>")
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(("\"disorder.h\"") "<smithwaterman/disorder.h>")
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(("Fasta.h") "fastahack/Fasta.h"))
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(for-each delete-file-recursively
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'("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
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"libVCFH" "multichoose" "smithwaterman"))))))
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(("\\$\\{TABIXPP_LIBRARIES\\}" text)
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(string-append "${FASTAHACK_LIBRARIES} "
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"${SMITHWATERMAN_LIBRARIES} "
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text)))
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(substitute* (find-files "." "\\.(h|c)(pp)?$")
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(("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
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(("\"convert.h\"") "<smithwaterman/convert.h>")
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(("\"disorder.h\"") "<smithwaterman/disorder.h>")
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(("Fasta.h") "fastahack/Fasta.h"))
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(for-each delete-file-recursively
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'("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
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"libVCFH" "multichoose" "smithwaterman"))))))
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(build-system cmake-build-system)
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(inputs
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(list bzip2
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@ -14608,39 +14608,39 @@ library automatically handles index file generation and use.")
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("intervaltree-src" ,(package-source intervaltree))
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("multichoose-src" ,(package-source multichoose))))
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(arguments
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`(#:tests? #f ; no tests
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'build-shared-library
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(lambda _
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(substitute* "CMakeLists.txt"
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(("vcflib STATIC") "vcflib SHARED"))
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(substitute* "test/Makefile"
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(("libvcflib.a") "libvcflib.so"))))
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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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(mkdir 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 "filevercmp-src" "filevercmp")
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(unpack "fsom-src" "fsom")
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(unpack "intervaltree-src" "intervaltree")
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(unpack "multichoose-src" "multichoose")))))
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;; This pkg-config file is provided by other distributions.
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(add-after 'install 'install-pkg-config-file
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(pkgconfig (string-append out "/lib/pkgconfig")))
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(mkdir-p pkgconfig)
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(with-output-to-file (string-append pkgconfig "/vcflib.pc")
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(list #:tests? #f ; no tests
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'build-shared-library
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(lambda _
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(format #t "prefix=~a~@
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(substitute* "CMakeLists.txt"
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(("vcflib STATIC") "vcflib SHARED"))
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(substitute* "test/Makefile"
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(("libvcflib.a") "libvcflib.so"))))
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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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(mkdir 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 "filevercmp-src" "filevercmp")
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(unpack "fsom-src" "fsom")
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(unpack "intervaltree-src" "intervaltree")
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(unpack "multichoose-src" "multichoose")))))
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;; This pkg-config file is provided by other distributions.
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(add-after 'install 'install-pkg-config-file
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(pkgconfig (string-append out "/lib/pkgconfig")))
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(mkdir-p pkgconfig)
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(with-output-to-file (string-append pkgconfig "/vcflib.pc")
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(lambda _
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(format #t "prefix=~a~@
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exec_prefix=${prefix}~@
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libdir=${exec_prefix}/lib~@
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includedir=${prefix}/include~@
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@ -14651,8 +14651,7 @@ library automatically handles index file generation and use.")
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Description: C++ library for parsing and manipulating VCF files~@
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Libs: -L${libdir} -lvcflib~@
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Cflags: -I${includedir}~%"
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out ,version)))
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#t))))))
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out #$version)))))))))
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(home-page "https://github.com/vcflib/vcflib/")
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(synopsis "Library for parsing and manipulating VCF files")
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(description "Vcflib provides methods to manipulate and interpret
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