bug#68381: closed ([PATCH] gnu: Add r-azimuth.)

[GNU bug Tracking System]

Your message dated Fri, 12 Jan 2024 13:40:38 +0100
with message-id <87o7dq4td5.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-azimuth.
has caused the debbugs.gnu.org bug report #68381,
regarding [PATCH] gnu: Add r-azimuth.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs@gnu.org.)


-- 
68381: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=68381
GNU Bug Tracking System
Contact help-debbugs@gnu.org with problems
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-azimuth.
>
>
>
>
> Date: 
>
> Thu, 11 Jan 2024 11:20:43 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (r-azimuth): New variable.
>
> Change-Id: I2b0d087378028663ee8d76ced8950f7a9721cb03
> ---
>  gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++
>  1 file changed, 60 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index f574fea0e9..9b45c54ef9 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -11171,6 +11171,66 @@ (define-public r-archr
>         "This package is designed to streamline scATAC analyses in R.")
>        (license license:gpl2+))))
>  
> +(define-public r-azimuth
> +  (let ((commit "243ee5db80fcbffa3452c944254a325a3da2ef9e")
> +        (revision "1"))
> +    (package
> +      (name "r-azimuth")
> +      (version (git-version "0.5.0" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/satijalab/azimuth";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "0vs4813kf2cv2j1z800ihwk62bw4dgmwgkd47rln58581chv39zm"))))
> +      (properties `((upstream-name . "Azimuth")))
> +      (build-system r-build-system)
> +      (propagated-inputs (list r-bsgenome-hsapiens-ucsc-hg38
> +                               r-dt
> +                               r-ensdb-hsapiens-v86
> +                               r-future
> +                               r-ggplot2
> +                               r-glmgampoi
> +                               r-googlesheets4
> +                               r-hdf5r
> +                               r-htmltools
> +                               r-httr
> +                               r-jaspar2020
> +                               r-jsonlite
> +                               r-matrix
> +                               r-patchwork
> +                               r-plotly
> +                               r-presto
> +                               r-rcpp
> +                               r-rlang
> +                               r-scales
> +                               r-seurat
> +                               r-seuratdata
> +                               r-seuratdisk
> +                               r-seuratobject
> +                               r-shiny
> +                               r-shinybs
> +                               r-shinydashboard
> +                               r-shinyjs
> +                               r-signac
> +                               r-stringr
> +                               r-tfbstools
> +                               r-withr))
> +      (home-page "https://github.com/satijalab/azimuth";)
> +      (synopsis
> +       "Shiny app showcasing a single-cell data query-reference mapping 
> algorithm")
> +      (description "Azimuth utilizes an annotated reference dataset.
> +It automates the processing, analysis, and interpretation.
> +This applies specifically to new single-cell RNA-seq or
> +ATAC-seq experiments.  Azimuth leverages a reference-based
> +mapping pipeline that inputs acounts matrix and performs
> +normalization, visualization, cell annotation, and
> +differential expression.")
> +      (license license:gpl3))))
> +
>  (define-public r-icellnet
>    ;; v1.0 tagged in 2020, last commit contains many fixes.
>    ;; DESCRIPTION says Version: 0.0.0.9000.
>
> base-commit: 6341dddcb9e7c8d555ea7294d61dcf64d775e032
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-azimuth.
>
>
>
>
> Date: 
>
> Fri, 12 Jan 2024 13:40:38 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.10.8; emacs 29.1
>
>
>
>
> Applied, thank you!
>
> -- 
> Ricardo
>
>
> --- End Message ---