guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 0ab540eb286dab276ee9746111284d62511b3d20
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Fri Feb 20 10:27:21 2026 +0100
gnu: r-voltron: Update to 0.2.3.
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.3.
[inputs]: Replace python with python-wrapper.
Change-Id: I180622af927e2386d45a4dadad4ebdad6e7ab6ac
---
gnu/packages/bioinformatics.scm | 248 ++++++++++++++++++++--------------------
1 file changed, 123 insertions(+), 125 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff002cacbb..0dfb5869cb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22831,137 +22831,135 @@ patterns.")
(license license:gpl3))))
(define-public r-voltron
- (let ((commit "1c0810b6603010af9afc7bb75eaebbe6de5ace30")
- (revision "1"))
- (package
- (name "r-voltron")
- (version (git-version "0.2.1" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/BIMSBbioinfo/VoltRon";)
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0w8lbk74n0pxz4rscl5vnfaw2xpl107y55cc5xff4km37dw901hv"))))
- (properties `((upstream-name . "VoltRon")))
- (build-system r-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- ;; By default VoltRon will use Basilisk, which uses Conda to set
- ;; up a Python environment. We override the fallback default
- ;; here. Users can still override the location of the Python
- ;; interpreter with the option "voltron.python.path".
- (add-after 'unpack 'do-not-use-conda
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "R/conversion.R"
- (("return\\(NULL\\)")
- (string-append
- "source(paste0(system.file(package=\"VoltRon\"),
\"/guix-refs.R\"));\n"
- "return(guix_python);")))))
- ;; We do this outside of the source code to ensure that
- ;; references are accessible to Guix.
- (add-after 'install 'record-python-reference
- (lambda* (#:key inputs #:allow-other-keys)
- (mkdir-p (string-append #$output "/site-library/VoltRon/"))
- (call-with-output-file (string-append #$output
"/site-library/VoltRon/guix-refs.R")
- (lambda (port)
- (format port "\
+ (package
+ (name "r-voltron")
+ (version "0.2.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BIMSBbioinfo/VoltRon";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "15cfszipvsq2c1gqkvvg5xkwndhjvn8hqjg5ymliwfcz9y9cv9xg"))))
+ (properties `((upstream-name . "VoltRon")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; By default VoltRon will use Basilisk, which uses Conda to set
+ ;; up a Python environment. We override the fallback default
+ ;; here. Users can still override the location of the Python
+ ;; interpreter with the option "voltron.python.path".
+ (add-after 'unpack 'do-not-use-conda
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "R/conversion.R"
+ (("return\\(NULL\\)")
+ (string-append
+ "source(paste0(system.file(package=\"VoltRon\"),
\"/guix-refs.R\"));\n"
+ "return(guix_python);")))))
+ ;; We do this outside of the source code to ensure that
+ ;; references are accessible to Guix.
+ (add-after 'install 'record-python-reference
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir-p (string-append #$output "/site-library/VoltRon/"))
+ (call-with-output-file (string-append #$output
"/site-library/VoltRon/guix-refs.R")
+ (lambda (port)
+ (format port "\
Sys.setenv(GUIX_PYTHONPATH=\"~a\");
guix_python <- \"~a\";"
- (getenv "GUIX_PYTHONPATH")
- (search-input-file inputs "/bin/python3")))))))))
- (inputs
- (list opencv
- ;; These Python inputs are used via reticulate.
- python
- python-numpy
- python-pandas
- python-anndata
- python-h5py
- python-natsort
- python-numcodecs
- python-packaging
- python-scipy
- python-tifffile
- python-zarr
- which ;tests/testthat/test_conversion.R
- zlib))
- (propagated-inputs (list r-biocsingular
- r-data-table
- r-dplyr
- r-ebimage
- r-ggplot2
- r-ggpubr
- r-ggrepel
- r-ids
- r-igraph
- r-irlba
- r-magick
- r-matrix
- r-pizzarr
- r-rann
- r-rcdt
- r-rcpp
- r-rcppannoy
- r-rcpparmadillo
- r-reshape2
- r-reticulate
- r-rhdf5
- r-rjson
- r-rlang
- r-s4arrays
- r-shiny
- r-shinyjs
- r-sp
- r-stringr
- r-uwot
-
- ;; Suggested packages
- r-anndata
- r-anndatar
- r-arrow
- r-bpcells
- r-circlize
- r-codetools
- r-complexheatmap
- r-delayedarray
- r-deseq2
- r-geojsonr
- r-ggforce
- r-ggnewscale
- r-giotto
- r-glmgampoi
- r-hdf5array
- r-hdf5dataframe
- r-imagearray
- r-music
- r-rhdf5
- r-rstudioapi
- r-s4vectors
- r-seurat
- r-seuratobject
- r-singlecellexperiment
- r-spacexr
- r-spatialexperiment
- r-summarizedexperiment
- r-viridislite
- r-vitesscer
- r-xml
- r-zarrdataframe))
- (native-inputs (list pkg-config r-testthat))
- (home-page "https://github.com/BIMSBbioinfo/VoltRon";)
- (synopsis "VoltRon for spatial data integration and analysis")
- (description
- "@code{VoltRon} is a novel spatial omic analysis toolbox for
+ (getenv "GUIX_PYTHONPATH")
+ (search-input-file inputs "/bin/python3")))))))))
+ (inputs
+ (list opencv
+ ;; These Python inputs are used via reticulate.
+ python-wrapper
+ python-numpy
+ python-pandas
+ python-anndata
+ python-h5py
+ python-natsort
+ python-numcodecs
+ python-packaging
+ python-scipy
+ python-tifffile
+ python-zarr
+ which ;tests/testthat/test_conversion.R
+ zlib))
+ (propagated-inputs (list r-biocsingular
+ r-data-table
+ r-dplyr
+ r-ebimage
+ r-ggplot2
+ r-ggpubr
+ r-ggrepel
+ r-ids
+ r-igraph
+ r-irlba
+ r-magick
+ r-matrix
+ r-pizzarr
+ r-rann
+ r-rcdt
+ r-rcpp
+ r-rcppannoy
+ r-rcpparmadillo
+ r-reshape2
+ r-reticulate
+ r-rhdf5
+ r-rjson
+ r-rlang
+ r-s4arrays
+ r-shiny
+ r-shinyjs
+ r-sp
+ r-stringr
+ r-uwot
+
+ ;; Suggested packages
+ r-anndata
+ r-anndatar
+ r-arrow
+ r-bpcells
+ r-circlize
+ r-codetools
+ r-complexheatmap
+ r-delayedarray
+ r-deseq2
+ r-geojsonr
+ r-ggforce
+ r-ggnewscale
+ r-giotto
+ r-glmgampoi
+ r-hdf5array
+ r-hdf5dataframe
+ r-imagearray
+ r-music
+ r-rhdf5
+ r-rstudioapi
+ r-s4vectors
+ r-seurat
+ r-seuratobject
+ r-singlecellexperiment
+ r-spacexr
+ r-spatialexperiment
+ r-summarizedexperiment
+ r-viridislite
+ r-vitesscer
+ r-xml
+ r-zarrdataframe))
+ (native-inputs (list pkg-config r-testthat))
+ (home-page "https://github.com/BIMSBbioinfo/VoltRon";)
+ (synopsis "VoltRon for spatial data integration and analysis")
+ (description
+ "@code{VoltRon} is a novel spatial omic analysis toolbox for
multi-omics integration using spatial image registration. @code{VoltRon} is
capable of analyzing multiple types and modalities of spatially-aware
datasets. @code{VoltRon} visualizes and analyzes regions of interests (ROIs),
spots, cells and even molecules.")
- (license license:expat))))
+ (license license:expat)))
(define-public r-zarrdataframe
(let ((commit "84c7db2f6f5f84b4a4308f8eb72bedc131fb68bc")
