bug#71339: closed ([PATCH] gnu: Add r-scent.)

[GNU bug Tracking System]

Your message dated Tue, 18 Jun 2024 09:27:34 +0200
with message-id <87y172zp5l.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-scent.
has caused the debbugs.gnu.org bug report #71339,
regarding [PATCH] gnu: Add r-scent.
to be marked as done.

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-- 
71339: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=71339
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-scent.
>
>
>
>
> Date: 
>
> Mon, 3 Jun 2024 14:19:55 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (r-scent): New variable.
>
> Change-Id: Ie517c0619683590f630013982e831fad528c1dea
> ---
>  gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
>  1 file changed, 37 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index cecd94bbb7..cdda029809 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1171,6 +1171,43 @@ (define-public r-scenic
>        ;; GPLv3.
>        (license license:gpl3))))
>  
> +(define-public r-scent
> +  (let ((commit "f01f18ac30f8a9bcf85b738c6c7815017e2c8ee5")
> +        (revision "1"))
> +    (package
> +      (name "r-scent")
> +      (version (git-version "1.0.0" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/immunogenomics/SCENT";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "18krksy8ac7yy8hghzaxscj91c61j195yg7j60zswdq97islvfzi"))))
> +      (properties `((upstream-name . "SCENT")))
> +      (build-system r-build-system)
> +      (inputs (list bedtools))
> +      (propagated-inputs (list r-boot
> +                               r-data-table
> +                               r-hmisc
> +                               r-lme4
> +                               r-mass
> +                               r-matrix
> +                               r-r-utils
> +                               r-stringr))
> +      (native-inputs (list r-knitr))
> +      (home-page "https://github.com/immunogenomics/SCENT";)
> +      (synopsis
> +       "Single-Cell enhancer target gene mapping for multimodal single-cell 
> data")
> +      (description
> +       "This package contains functions for the SCENT algorithm.
> +SCENT uses single-cell multimodal data and links ATAC-seq peaks
> +to their target genes by modeling association between chromatin
> +accessibility and gene expression across individual single cells.")
> +      (license license:expat))))
> +
>  (define-public r-saige
>    (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167")
>          (revision "1"))
>
> base-commit: 1615084a9a4115d48b75b3db048761e7534efc87
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-scent.
>
>
>
>
> Date: 
>
> Tue, 18 Jun 2024 09:27:34 +0200
>
>
>
>
> Thanks for the patch.  Applied!
>
> -- 
> Ricardo
>
>
> --- End Message ---