diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3364a357fb..43835cfb88 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -40,6 +40,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system haskell) + #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) @@ -477,6 +478,62 @@ BED, GFF/GTF, VCF.") (base32 "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5")))))) +(define-public pbbam + (package + (name "pbbam") + (version "0.23.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/pbbam.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0h9gkrpf2lrxklxp72xfl5bi3h5zcm5hprrya9gf0hr3xwlbpp0x")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (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* "tests/meson.build" + (("pbbam_gtest_dep = dependency\\('gtest_main'.*") + (format #f "cpp = meson.get_compiler('cpp') +pbbam_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" + (assoc-ref inputs "googletest")))) + #t))) + ;; TODO: tests/pbbam_test cannot be linked + ;; ld: tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o: + ;; undefined reference to symbol '_ZTIN7testing4TestE' + ;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so: + ;; error adding symbols: DSO missing from command line + #:tests? #f + #:configure-flags '("-Dtests=false"))) + ;; These libraries are listed as "Required" in the pkg-config file. + (propagated-inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (inputs + `(("boost" ,boost) + ("samtools" ,samtools))) + (native-inputs + `(("googletest" ,googletest) + ("pkg-config" ,pkg-config) + ("python" ,python-wrapper))) ; for tests + (home-page "https://github.com/PacificBiosciences/pbbam") + (synopsis "Work with PacBio BAM files") + (description + "The pbbam software package provides components to create, query, and +edit PacBio BAM files and associated indices. These components include a core +C++ library, bindings for additional languages, and command-line utilities. +This library is not intended to be used as a general-purpose BAM utility - all +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 ribotaper (package (name "ribotaper") |