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spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.60 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=a+F5A2Yn; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 253E42AF38 X-Spam-Score: 7.60 X-Migadu-Scanner: scn0.migadu.com X-TUID: hz4NBYHg7yvI X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-multivelo): New variable. --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2de09aa32..d7426c0ac9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10540,6 +10540,68 @@ (define-public python-biothings-client API services.") (license license:bsd-3))) +(define-public python-multivelo + (package + (name "python-multivelo") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "multivelo" version)) + (sha256 + (base32 + "1b4qyngwagh5sc2ygyfqyirg63myzh1g1glk03a1ykxfii32cjlp")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f ;pypi source does not contains tests + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (for-each + (lambda (wheel) + (format #t wheel) + (invoke "python" "-m" "pip" "install" + wheel (string-append "--prefix=" #$output))) + (find-files "dist" "\\.whl$")))) + (add-before 'sanity-check 'set-env + (lambda _ + ;; /homeless-shelter/.config/matplotlib is not a writable directory; + (setenv "MPLCONFIGDIR" "/tmp") + ;; numba RuntimeError: cannot cache function 'rdist' + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (native-inputs (list python-pypa-build)) + (propagated-inputs + (list python-anndata + python-h5py + python-ipywidgets + python-joblib + python-loompy + python-matplotlib + python-numba + python-numpy + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-seaborn + python-tqdm + python-umap-learn + scvelo)) + (home-page "https://github.com/welch-lab/MultiVelo") + (synopsis "Velocity inference from single-cell multi-omic data") + (description "@code{MultiVelo} uses a probabilistic latent variable model +to estimate the switch time and rate parameters of gene regulation, providing a +quantitative summary of the temporal relationship between epigenomic and +transcriptomic changes.") + (license license:bsd-3))) + (define-public python-mygene (package (name "python-mygene") base-commit: 3734857fc55df2c599c2fe5cc4ae49f5d47879fc -- 2.37.3