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| author | Ricardo Wurmus <rekado@elephly.net> | 2023-05-05 15:36:40 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-05-05 15:39:29 +0200 |
| commit | 931650212a31e2c7c80e490e084e79754ea6c0a7 (patch) | |
| tree | 5ccf5fa4cf4af0549232d70bda698da870a719e0 | |
| parent | 0b5088a2a3c7f78b79d3619a7be321d625514223 (diff) | |
| download | guix-931650212a31e2c7c80e490e084e79754ea6c0a7.tar guix-931650212a31e2c7c80e490e084e79754ea6c0a7.tar.gz | |
gnu: Add python-biofluff.
* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 474b955bd0..e48b340a3a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1251,6 +1251,54 @@ Format (GFF) with Biopython integration.") (modify-inputs (package-propagated-inputs python-bcbio-gff) (replace "python-biopython" python-biopython-1.73))))) +;; Note: the name on PyPi is "biofluff". +(define-public python-biofluff + (package + (name "python-biofluff") + (version "3.0.4") + ;; PyPi tarball does not contain test data. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/simonvh/fluff") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12yvhgp72s2ygf3h07rrc852zd6q8swc41hm28mcczpsyprggxyz")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Theses tests require internet access + '(list "--ignore=tests/test_mirror.py" + "-k" "not test_plots_big") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'matplotlib-compatibility + (lambda _ + (substitute* "fluff/plot.py" + (("beginarrow=False, endarrow=True,") ""))))))) + (propagated-inputs + (list htseq + python-matplotlib + python-numpy + python-palettable + python-pybedtools + python-pybigwig + python-pysam + python-scikit-learn + python-scipy)) + (native-inputs + (list python-pytest)) + (home-page "https://github.com/simonvh/fluff/") + (synopsis "Analysis and visualization of high-throughput sequencing data") + (description + "Fluff is a Python package that contains several scripts to produce +pretty, publication-quality figures for next-generation sequencing +experiments.") + (license license:expat))) + (define-public python-cellbender (package (name "python-cellbender") |