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branch master updated: gnu: Add python-multivelo.
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guix-commits |
Subject: |
branch master updated: gnu: Add python-multivelo. |
Date: |
Thu, 27 Oct 2022 09:16:21 -0400 |
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rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new fe7b421d05 gnu: Add python-multivelo.
fe7b421d05 is described below
commit fe7b421d0520bdbfc28db4b7b3a82c63e2d50330
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Sun Oct 23 23:37:21 2022 +0200
gnu: Add python-multivelo.
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
---
gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 59 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index da57868284..d431e467ed 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10540,6 +10540,65 @@ single-cell RNA-seq data.")
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 contain 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 _
+ (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 _
+ ;; 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 "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")
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