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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 62 |
1 files changed, 62 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 43835cfb88..da12a145c5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -534,6 +534,68 @@ input and output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.") (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 (package (name "ribotaper") |