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02/05: gnu: Add python-bulkvis.
From: |
guix-commits |
Subject: |
02/05: gnu: Add python-bulkvis. |
Date: |
Mon, 5 Jun 2023 11:11:51 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 6559adea29ae116f5fa882f88678e510001e2c88
Author: Navid Afkhami <navid.afkhami@mdc-berlin.de>
AuthorDate: Mon Jun 5 17:05:35 2023 +0200
gnu: Add python-bulkvis.
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
gnu/packages/bioinformatics.scm | 68 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 68 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 251e46061f..5667fba689 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1337,6 +1337,74 @@ pretty, publication-quality figures for next-generation
sequencing
experiments.")
(license license:expat)))
+(define-public python-bulkvis
+ (let ((commit "00a82a90c7e748a34af896e779d27e78a2c82b5e")
+ (revision "2"))
+ (package
+ (name "python-bulkvis")
+ (version (git-version "2.0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/LooseLab/bulkVis")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "02blai158xyyqcg0ljzkmfa6ci05m4awrl4njvp9nwfp717xq8n0"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* '("requirements.txt"
+ "setup.py")
+ (("tqdm~=4.46.1") "tqdm")
+ (("tornado~=6.0.4") "tornado")
+ (("pandas~=1.0.5") "pandas")
+ (("h5py~=2.10.0") "h5py")
+ ;; See below for com
+ (("bokeh~=2.1.0") "bokeh")))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f ;There are no tests
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'bokeh-compatibility
+ (lambda _
+ (substitute* "bulkvis/bulkvis.py"
+ (("import importlib" m)
+ (string-append m "
+from bokeh.command.subcommand import Argument
+from bokeh.util.dataclasses import entries\n"))
+ (("( *)_parser.add_argument" m indent)
+ (string-append
+ (string-join (list "if isinstance(opts, Argument):\n"
+ " opts = dict(entries(opts))\n")
+ indent 'prefix)
+ m))))))))
+ (propagated-inputs (list python-bokeh
+ python-dill
+ python-h5py
+ python-joblib
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-plotly
+ python-readpaf
+ python-scikit-learn
+ python-scikit-image
+ python-scipy
+ python-seaborn
+ python-tornado-6
+ python-tqdm
+ python-umap-learn))
+ (native-inputs (list python-pytest))
+ (home-page "https://github.com/LooseLab/bulkVis")
+ (synopsis "Interactive visualization of bulk RNA-seq data")
+ (description
+ "This is a Python package for the interactive visualization of bulk
+RNA-seq data. It provides a range of plotting functions and interactive tools
+to explore and analyze bulk RNA-seq data.")
+ (license license:expat))))
+
(define-public python-cell2cell
(package
(name "python-cell2cell")