bug#65688: closed ([PATCH 2/2] gnu: Add r-trackviewer.)

[GNU bug Tracking System]

Your message dated Sat, 02 Sep 2023 11:55:55 +0200
with message-id <87h6ocdhj3.fsf@elephly.net>
and subject line [PATCH 2/2] gnu: Add r-trackviewer.
has caused the debbugs.gnu.org bug report #65688,
regarding [PATCH 2/2] gnu: Add r-trackviewer.
to be marked as done.

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-- 
65688: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=65688
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH 2/2] gnu: Add r-trackviewer.
>
>
>
>
> Date: 
>
> Fri, 1 Sep 2023 20:45:12 +0000
>
>
>
>
> * gnu/packages/bioconductor.scm (r-trackviewer): New variable.
> ---
>  gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
>  1 file changed, 42 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 88592c4f71..0070d7777c 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -9931,6 +9931,48 @@ (define-public r-tkwidgets
>       "This package implements widgets to provide user interfaces.")
>      (license license:artistic2.0)))
>  
> +(define-public r-trackviewer
> +  (package
> +    (name "r-trackviewer")
> +    (version "1.36.2")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (bioconductor-uri "trackViewer" version))
> +              (sha256
> +               (base32
> +                "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))))
> +    (properties `((upstream-name . "trackViewer")))
> +    (build-system r-build-system)
> +    (propagated-inputs (list r-annotationdbi
> +                             r-biocgenerics
> +                             r-genomeinfodb
> +                             r-genomicalignments
> +                             r-genomicfeatures
> +                             r-genomicranges
> +                             r-graph
> +                             r-grimport
> +                             r-gviz
> +                             r-htmlwidgets
> +                             r-interactionset
> +                             r-iranges
> +                             r-plotrix
> +                             r-rgraphviz
> +                             r-rhdf5
> +                             r-rsamtools
> +                             r-rtracklayer
> +                             r-s4vectors
> +                             r-scales
> +                             r-strawr))
> +    (native-inputs (list esbuild r-knitr))
> +    (home-page "https://bioconductor.org/packages/trackViewer";)
> +    (synopsis "Web interface for interactive multi-omics data analysis")
> +    (description
> +     "TrackViewer offers multi-omics analysis with web based  tracks and 
> lollipops.
> +Visualize mapped reads along with annotation as track layers for NGS dataset
> +such as @code{ChIP-seq,} RNA-seq, @code{miRNA-seq,} DNA-seq, SNPs and
> +methylation data.")
> +    (license license:gpl2+)))
> +
>  (define-public r-transcriptr
>    (package
>      (name "r-transcriptr")
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH 2/2] gnu: Add r-trackviewer.
>
>
>
>
> Date: 
>
> Sat, 02 Sep 2023 11:55:55 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.10.5; emacs 28.2
>
>
>
>
> Thanks for the patch!
>
> This one needed a little more work.  The “esbuild” in the native inputs
> was added by the importer because the package includes minified
> JavaScript files.
>
> Luckily it’s just one file and we can replace it easily.  I’ve made the
> necessary changes and pushed it with commit
> 8c0c94bf9f70a9252cd6f4261d2bce6bdba2bd0b to the “master” branch.
>
> -- 
> Ricardo
>
>
> --- End Message ---