gnu: Add blasr-libcpp.

* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
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Ricardo Wurmus 2019-03-18 14:38:10 +01:00 committed by Ricardo Wurmus
parent 55154c5f40
commit 6a6cd48cf0
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@ -534,6 +534,68 @@ (define-public pbbam
Non-PacBio BAMs will cause exceptions to be thrown.") Non-PacBio BAMs will cause exceptions to be thrown.")
(license license:bsd-3))) (license license:bsd-3)))
(define-public blasr-libcpp
(package
(name "blasr-libcpp")
(version "5.3.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/blasr_libcpp.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0cn5l42zyq67sj0g2imqkhayz2iqvv0a1pgpbmlq0qynjmsrbfd2"))))
(build-system meson-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'link-with-hdf5
(lambda* (#:key inputs #:allow-other-keys)
(let ((hdf5 (assoc-ref inputs "hdf5")))
(substitute* "meson.build"
(("libblasr_deps = \\[" m)
(string-append
m
(format #f "cpp.find_library('hdf5', dirs : '~a'), \
cpp.find_library('hdf5_cpp', dirs : '~a'), "
hdf5 hdf5)))))
#t))
(add-after 'unpack 'find-googletest
(lambda* (#:key inputs #:allow-other-keys)
;; It doesn't find gtest_main because there's no pkg-config file
;; for it. Find it another way.
(substitute* "unittest/meson.build"
(("libblasr_gtest_dep = dependency\\('gtest_main'.*")
(format #f "cpp = meson.get_compiler('cpp')
libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
(assoc-ref inputs "googletest"))))
#t)))
;; TODO: unittest/libblasr_unittest cannot be linked
;; ld: ;; unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o:
;; undefined reference to symbol
;; '_ZN7testing8internal9DeathTest6CreateEPKcPKNS0_2REES3_iPPS1_'
;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so:
;; error adding symbols: DSO missing from command line
#:tests? #f
#:configure-flags '("-Dtests=false")))
(inputs
`(("boost" ,boost)
("hdf5" ,hdf5)
("pbbam" ,pbbam)
("zlib" ,zlib)))
(native-inputs
`(("googletest" ,googletest)
("pkg-config" ,pkg-config)))
(home-page "https://github.com/PacificBiosciences/blasr_libcpp")
(synopsis "Library for analyzing PacBio genomic sequences")
(description
"This package provides three libraries used by applications for analyzing
PacBio genomic sequences. This library contains three sub-libraries: pbdata,
hdf and alignment.")
(license license:bsd-3)))
(define-public ribotaper (define-public ribotaper
(package (package
(name "ribotaper") (name "ribotaper")