Mădălin Ionel Patrașcu wrote 2 years ago
(address . guix-patches@gnu.org)
20221023213721.20059-1-madalinionel.patrascu@mdc-berlin.de
X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
---
gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++
1 file changed, 62 insertions(+)
Toggle diff (77 lines)
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