bug#38259: closed ([PATCH] gnu: Add r-harmony.)

[GNU bug Tracking System]

Your message dated Thu, 21 Nov 2019 11:21:44 +0100
with message-id <address@hidden>
and subject line Re: [bug#38259] [PATCH]  gnu: Add r-harmony.
has caused the debbugs.gnu.org bug report #38259,
regarding [PATCH]  gnu: Add r-harmony.
to be marked as done.

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-- 
38259: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=38259
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH]  gnu: Add r-harmony.
>
>
>
>
> Date: 
>
> Mon, 18 Nov 2019 18:22:16 +0100
>
>
>
>
>     * gnu/packages/bioinformatics.scm (r-harmony): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++-
>  1 file changed, 37 insertions(+), 1 deletion(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 07c70fb82c..5da95d66a6 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -11,7 +11,7 @@
>  ;;; Copyright © 2017 Arun Isaac <address@hidden>
>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <address@hidden>
>  ;;; Copyright © 2018 Gábor Boskovits <address@hidden>
> -;;; Copyright © 2018 Mădălin Ionel Patrașcu <address@hidden>
> +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <address@hidden>
>  ;;; Copyright © 2019 Maxim Cournoyer <address@hidden>
>  ;;; Copyright © 2019 Brian Leung <address@hidden>
>  ;;;
> @@ -15349,3 +15349,39 @@ methylation metrics from them.  MethylDackel requires 
> an indexed fasta file
>  containing the reference genome as well.")
>      ;; See https://github.com/dpryan79/MethylDackel/issues/85
>      (license license:expat)))
> +
> +(define-public r-harmony
> +  (let ((commit "1a6d77aae524a08a2ca91737a152ab2047ccee78")
> +        (revision "1"))
> +    (package
> +      (name "r-harmony")
> +      (version (git-version "1.0" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/immunogenomics/harmony.git";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "1905qsbl5iv3kxki73gmyzshyb8zc6asdaymywndscn7mjkwm7aw"))))
> +      (build-system r-build-system)
> +      (propagated-inputs
> +       `(("r-cowplot" ,r-cowplot)
> +         ("r-dplyr" ,r-dplyr)
> +         ("r-ggplot2" ,r-ggplot2)
> +         ("r-irlba" ,r-irlba)
> +         ("r-matrix" ,r-matrix)
> +         ("r-rcpp" ,r-rcpp)
> +         ("r-rcpparmadillo" ,r-rcpparmadillo)
> +         ("r-rcppprogress" ,r-rcppprogress)
> +         ("r-rlang" ,r-rlang)
> +         ("r-tibble" ,r-tibble)
> +         ("r-tidyr" ,r-tidyr)))
> +      (home-page "https://github.com/immunogenomics/harmony.git";)
> +      (synopsis "Fast, sensitive, and accurate integration of single cell 
> data")
> +      (description
> +       "Harmony software is the R implementation of the algorithm with the same
> +name for single cell integration, described in Korsunsky et al 2018.  Package
> +includes a standalone Harmony function and interfaces to external frameworks.")
> +      (license license:gpl3))))
> -- 
> 2.17.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#38259] [PATCH]  gnu: Add r-harmony.
>
>
>
>
> Date: 
>
> Thu, 21 Nov 2019 11:21:44 +0100
>
>
>
>
> User-agent: 
>
> Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux)
>
>
>
>
> Hello Mădălin,
>
> Mădălin Ionel Patrașcu <address@hidden> skribis:
>
> >     * gnu/packages/bioinformatics.scm (r-harmony): New variable.
>
> Applied with the changes below.
>
> Thank you!
>
> Ludo’.
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 5da95d66a6..d1d17dc3d5 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -15382,6 +15382,6 @@ containing the reference genome as well.")
>        (synopsis "Fast, sensitive, and accurate integration of single cell 
> data")
>        (description
>         "Harmony software is the R implementation of the algorithm with the same
> -name for single cell integration, described in Korsunsky et al 2018.  Package
> +name for single cell integration, described in Korsunsky et al 2018.  The 
> package
>  includes a standalone Harmony function and interfaces to external frameworks.")
> -      (license license:gpl3))))
> +      (license license:gpl3+))))
>
> --- End Message ---