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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2019-03-18 14:38:19 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-03-18 14:47:49 +0100 |
| commit | f88bdc5ff91583f587d3b8a110e73f949bedb58e (patch) | |
| tree | cfdd48cb37d08510c5cf832775454897f378b719 /gnu | |
| parent | 6a6cd48cf0784c46c5bb05668c2e423fdff5dca5 (diff) | |
| download | patches-f88bdc5ff91583f587d3b8a110e73f949bedb58e.tar patches-f88bdc5ff91583f587d3b8a110e73f949bedb58e.tar.gz | |
gnu: Add blasr.
* gnu/packages/bioinformatics.scm (blasr): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index da12a145c5..498ebc38b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -596,6 +596,51 @@ PacBio genomic sequences. This library contains three sub-libraries: pbdata, hdf and alignment.") (license license:bsd-3))) +(define-public blasr + (package + (name "blasr") + (version "5.3.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/blasr.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1skgy2mvz8gsgfh1gc2nfgwvpyzb1hpmp2cf2773h5wsj8nw22kl")))) + (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" + (("blasr_deps = \\[" m) + (string-append + m + (format #f "cpp.find_library('hdf5', dirs : '~a'), \ +cpp.find_library('hdf5_cpp', dirs : '~a'), " + hdf5 hdf5))))) + #t))) + ;; Tests require "cram" executable, which is not packaged. + #:tests? #f + #:configure-flags '("-Dtests=false"))) + (inputs + `(("boost" ,boost) + ("blasr-libcpp" ,blasr-libcpp) + ("hdf5" ,hdf5) + ("pbbam" ,pbbam) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "") + (synopsis "PacBio long read aligner") + (description + "Blasr is a genomic sequence aligner for processing PacBio long reads.") + (license license:bsd-3))) + (define-public ribotaper (package (name "ribotaper") |