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-rw-r--r--gnu/packages/bioinformatics.scm47
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7dec74f0c0..afbacc1c83 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15065,6 +15065,53 @@ line, interactively explore genomic data within Jupyter environment or web
browser.")
(license license:gpl3+)))
+(define-public python-pyspoa
+ (package
+ (name "python-pyspoa")
+ (version "0.0.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/nanoporetech/pyspoa")
+ (commit (string-append "v" version))
+ (recursive? #true)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1lgf2shzhxkcsircd6vy46h27pjljd5q95fyz1cm3lkk702qbnzx"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'build-libspoa
+ (lambda _
+ (mkdir-p "src/build")
+ (with-directory-excursion "src/build"
+ (invoke "cmake"
+ "-Dspoa_optimize_for_portability=ON"
+ "-DCMAKE_BUILD_TYPE=Release"
+ "-DCMAKE_CXX_FLAGS=\"-I ../vendor/cereal/include/\" -fPIC"
+ "..")
+ (invoke "make"))))
+ (replace 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "tests/test_pyspoa.py")))))))
+ (propagated-inputs
+ `(("pybind11" ,pybind11)))
+ (native-inputs
+ `(("cmake" ,cmake-minimal)))
+ (home-page "https://github.com/nanoporetech/pyspoa")
+ (synopsis "Python bindings for the SIMD partial order alignment library ")
+ (description
+ "This package provides Python bindings for spoa, a C++ implementation of
+the @dfn{partial order alignment} (POA) algorithm (as described in
+10.1093/bioinformatics/18.3.452) which is used to generate consensus
+sequences")
+ (license license:expat)))
+
(define-public scregseg
(package
(name "scregseg")