diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7ea856c157..c70dcdf93b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1255,6 +1255,66 @@ servers supporting the protocol.") genomics data.") (license license:bsd-3))) +(define-public python-phenograph + (package + (name "python-phenograph") + (version "1.5.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "PhenoGraph" version)) + (sha256 + (base32 + "0nji449mzwgp1f87iknl5fmnjdkrhkfkapxvafxdw01s0jg8zcj6")) + (modules '((guix build utils))) + ;; Remove bundled binaries + (snippet + '(delete-file-recursively "phenograph/louvain")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; This test can never succeed because Q_leiden is never set to + ;; anything other than None. + (add-after 'unpack 'disable-leiden-test + (lambda _ + (substitute* "tests/test_cluster.py" + (("def test_run_leiden") "def _test_run_leiden")))) + (add-after 'unpack 'patch-louvain + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "phenograph/core.py" + (("lpath = os.path.*") + (string-append "lpath = \"" + (dirname (search-input-file inputs "/bin/community")) + "\"\n")) + (("linux-(community|hierarchy|convert)" _ thing) thing) + ;; Do not write binaries, because the unmodified "convert" + ;; from louvain only knows how to process plain text files. + (("with open\\(filename \\+ \".bin\", \"w\\+b\"\\) as f:") + "with open(filename + \".bin\", \"w+\") as f:") + (("f.writelines\\(\\[e for t in zip\\(ij, s\\) for e in t\\]\\)") + "for [src, dest], weight in zip(ij, s): \ +f.write(src.astype(\"str\") + ' ' + \ +dest.astype(\"str\") + ' ' + \ +weight.astype(\"str\") + '\\n')"))))))) + (inputs + (list louvain)) + (propagated-inputs + (list python-leidenalg + python-numpy + python-psutil + python-scikit-learn + python-scipy)) + (native-inputs + (list python-pytest)) + (home-page "https://github.com/dpeerlab/PhenoGraph.git") + (synopsis "Graph-based clustering for high-dimensional single-cell data") + (description + "PhenoGraph is a clustering method designed for high-dimensional +single-cell data. It works by creating a graph representing phenotypic +similarities between cells and then identifying communities in this graph.") + (license license:expat))) + (define-public python-phylophlan (package (name "python-phylophlan") |