bug#52463: closed ([PATCH] gnu: Add r-chromvarmotifs.)

[GNU bug Tracking System]

Your message dated Mon, 13 Dec 2021 12:38:34 +0000
with message-id <87r1agn0fz.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-chromvarmotifs.
has caused the debbugs.gnu.org bug report #52463,
regarding [PATCH] gnu: Add r-chromvarmotifs.
to be marked as done.

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-- 
52463: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=52463
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-chromvarmotifs.
>
>
>
>
> Date: 
>
> Mon, 13 Dec 2021 12:52:07 +0100
>
>
>
>
> * gnu/packages/bioconductor.scm (r-chromvarmotifs): New variable.
> This package is not a bioconductor one, but it use the r-tfbstools
> that is stored in bioconductor.scm.  If I used the cran.scm for the
> current definition I should import the bioconductor and it already
> imports cran.  Beside this the package is somehow related with other
> bioconductor packages.
> ---
>  gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
>  1 file changed, 29 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 44bf5c7d24..28cc8b7458 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -1183,6 +1183,35 @@ (define-public r-chromstardata
>  chromstaR package.")
>      (license license:gpl3)))
>  
> +(define-public r-chromvarmotifs
> +  (let
> +      ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
> +       (revision "1"))
> +    (package
> +      (name "r-chromvarmotifs")
> +      (version (git-version "0.2.0" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/GreenleafLab/chromVARmotifs";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q"))))
> +      (properties `((upstream-name . "chromVARmotifs")))
> +      (build-system r-build-system)
> +      (propagated-inputs
> +       `(("r-tfbstools" ,r-tfbstools)))
> +      (home-page "https://github.com/GreenleafLab/chromVARmotifs";)
> +      (synopsis "Stores motif collections for use with motifmatchr or 
> chromVAR")
> +      (description
> +       "This package @code{r-chromvarmotifs} stores motifs collections as
> +lists of @dfn{position frequency matrix} (PWMatrixList) objects provided by
> +@code{TFBSTools} package for use in R with packages like @code{motifmatchr} or
> +@code{chromVAR}.")
> +      (license license:expat))))
> +
>  (define-public r-copyhelper
>    (package
>      (name "r-copyhelper")
> -- 
> 2.34.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-chromvarmotifs.
>
>
>
>
> Date: 
>
> Mon, 13 Dec 2021 12:38:34 +0000
>
>
>
>
> User-agent: 
>
> mu4e 1.6.6; emacs 28.0.50
>
>
>
>
> Applied to the “master” branch with commit
> 5f32468acfc7ae3a7dd736810ab0c3cdde7310da.  Thanks!
>
> -- 
> Ricardo
>
>
> --- End Message ---