Subject: Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.

From: zimoun <[email-masked]>
Date: Tue, 22 Dec 2020 19:15:41 +0100

Hi Aniket,

(CC Ricardo since it could provide the correct gitlogy magic :-))

The patch does not apply because the file gnu/packages/cran.scm changed
in the meantime.  I am sorry that we have not been enough reactive.

However, when creating the patch, you had used the option ’--base’;
which really helps because I would be able to apply it and rebase
myself.

Currently, I do not know how to do without copy/pasting by hand, so
loosing your authorship.  Could you rebase on the top of master?

If you cannot, no worry.  Just let me know.

Ricardo, any tip to bypass this kind of issue?

On Thu, 29 Oct 2020 at 22:39, Aniket Patil <[email-masked]> wrote:
> * gnu/packages/cran.scm (r-deconstructsigs): New variable.
> ---
>  gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
>  1 file changed, 30 insertions(+)
>
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index 82caaf54f6..75d9ae7de2 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -24715,3 +24715,33 @@ modal regression and conditional density estimation in the
>  presence/absence of measurement error. Bandwidth selection is 
>  also provided for each method.")
>      (license license:gpl2+)))
> +
> +(define-public r-deconstructsigs
> +  (package
> +    (name "r-deconstructsigs")
> +    (version "1.8.0")
> +    (source
> +      (origin
> +        (method url-fetch)
> +        (uri (cran-uri "deconstructSigs" version))
> +        (sha256
> +          (base32
> +            "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
> +    (properties
> +      `((upstream-name . "deconstructSigs")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +      `(("r-bsgenome" ,r-bsgenome)
> +        ("r-bsgenome-hsapiens-ucsc-hg19"
> +         ,r-bsgenome-hsapiens-ucsc-hg19)
> +        ("r-genomeinfodb" ,r-genomeinfodb)
> +        ("r-reshape2" ,r-reshape2)))
> +    (home-page
> +      "https://github.com/raerose01/deconstructSigs")
> +    (synopsis "Identifies Signatures Present in a Tumor Sample")
> +    (description
> +      "Takes sample information in the form of the fraction of 
> +mutations in each of 96 trinucleotide contexts and identifies 
> +the weighted combination of published signatures that, when summed, 
> +most closely reconstructs the mutational profile.")
> +    (license license:gpl2+)))

Cheers,
simon