bug#65493: closed ([PATCH] gnu: Add r-msigdb.)

[GNU bug Tracking System]

Your message dated Mon, 28 Aug 2023 10:06:47 +0200
with message-id <87h6ojfv3l.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-msigdb.
has caused the debbugs.gnu.org bug report #65493,
regarding [PATCH] gnu: Add r-msigdb.
to be marked as done.

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-- 
65493: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=65493
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-msigdb.
>
>
>
>
> Date: 
>
> Thu, 24 Aug 2023 10:38:37 +0000
>
>
>
>
> * gnu/packages/bioconductor.scm (r-msigdb): New variable.
> ---
>  gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
>  1 file changed, 33 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 74071900a3..5e323d11ef 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -1754,6 +1754,39 @@ (define-public r-msdata
>  files for various search engines.")
>      (license license:gpl2+)))
>  
> +(define-public r-msigdb
> +  (package
> +    (name "r-msigdb")
> +    (version "1.8.0")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (bioconductor-uri "msigdb" version
> +                                     'experiment))
> +              (sha256
> +               (base32
> +                "1kgsqg1d5r852qas09g6fs0pcmk6jgbb6g983v6iqw19qsiy6jby"))))
> +    (properties `((upstream-name . "msigdb")))
> +    (build-system r-build-system)
> +    (propagated-inputs (list r-annotationdbi
> +                             r-annotationhub
> +                             r-experimenthub
> +                             r-gseabase
> +                             r-org-hs-eg-db
> +                             r-org-mm-eg-db))
> +    (native-inputs (list r-knitr))
> +    (home-page "https://davislaboratory.github.io/msigdb";)
> +    (synopsis "ExperimentHub package for the molecular signatures database")
> +    (description
> +     "R-msigdb provides the Molecular Signatures Database in a R accessible 
> objects.
> +Signatures are stored in @code{GeneSet} class objects form
> +the GSEABase package and the entire database is stored in a
> +@code{GeneSetCollection} object.  These data are then hosted
> +on the @code{ExperimentHub.} Data used in this package was
> +obtained from the @code{MSigDB} of the Broad Institute.
> +Metadata for each gene set is stored along with the gene
> +set in the @code{GeneSet} class object.")
> +    (license license:cc-by4.0)))
> +
>  (define-public r-pasilla
>    (package
>      (name "r-pasilla")
>
> base-commit: 160f78a4d92205df986ed9efcce7d3aac188cb24
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-msigdb.
>
>
>
>
> Date: 
>
> Mon, 28 Aug 2023 10:06:47 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.10.5; emacs 28.2
>
>
>
>
> Applied with minor changes:
>
> - changed the home page because it is not reachable (guix lint
>   complained)
> - reflowed the description
>
> Thanks!
>
> -- 
> Ricardo
>
>
> --- End Message ---