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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-08-27 14:28:28 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-08-30 18:29:56 +0200 |
| commit | e85b35070caa41926b52625ef0fa828d6acc8271 (patch) | |
| tree | 35249804f71a256a0c345f70936d7785af978c75 | |
| parent | b8926ca6178e19d2add07593390409226383ed7e (diff) | |
| download | guix-e85b35070caa41926b52625ef0fa828d6acc8271.tar.gz | |
gnu: Add python-pybbi.
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0979a86d8d..5d4b4e1316 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14795,6 +14795,53 @@ instruments, or Pacific Biosciences RSII or Sequel sequencers.") data from @file{.hic} files. This package provides Python bindings.") (license license:expat))) +(define-public python-pybbi + (package + (name "python-pybbi") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pybbi" version)) + (sha256 + (base32 + "1hvy2f28i2b41l1pq15vciqbj538n0lichp8yr6413jmgg06xdsk")))) + (build-system python-build-system) + (arguments + `(#:tests? #false ; tests require network access + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-cc + (lambda _ (setenv "CC" "gcc"))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (copy-recursively "tests" "/tmp/tests") + (with-directory-excursion "/tmp/tests" + (invoke "python" "-m" "pytest" "-v")))))))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("python-pkgconfig" ,python-pkgconfig) + ("python-pytest" ,python-pytest))) + (inputs + `(("libpng" ,libpng) + ("openssl" ,openssl) + ("zlib" ,zlib))) + (propagated-inputs + `(("python-cython" ,python-cython) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-six" ,python-six))) + (home-page "https://github.com/nvictus/pybbi") + (synopsis "Python bindings to UCSC Big Binary file library") + (description + "This package provides Python bindings to the UCSC Big +Binary (bigWig/bigBed) file library. This provides read-level access to local +and remote bigWig and bigBed files but no write capabilitites. The main +feature is fast retrieval of range queries into numpy arrays.") + (license license:expat))) + (define-public r-ascat (package (name "r-ascat") |