summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2019-03-18 14:38:10 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-18 14:47:45 +0100
commit6a6cd48cf0784c46c5bb05668c2e423fdff5dca5 (patch)
tree92b63bccbb40bab20f76183eb1822b070773fe63
parent55154c5f40d0b2782f98f5e2431f3c845ed798cd (diff)
downloadpatches-6a6cd48cf0784c46c5bb05668c2e423fdff5dca5.tar
patches-6a6cd48cf0784c46c5bb05668c2e423fdff5dca5.tar.gz
gnu: Add blasr-libcpp.
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm62
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")