bug#65364: closed ([PATCH] gnu: Add python-scDamAndTools.)

[GNU bug Tracking System]

Your message dated Mon, 28 Aug 2023 09:51:53 +0200
with message-id <87y1hvfvt1.fsf@elephly.net>
and subject line [PATCH] gnu: Add python-scDamAndTools.
has caused the debbugs.gnu.org bug report #65364,
regarding [PATCH] gnu: Add python-scDamAndTools.
to be marked as done.

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-- 
65364: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=65364
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add python-scDamAndTools.
>
>
>
>
> Date: 
>
> Fri, 18 Aug 2023 14:01:06 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (python-scDamAndTools): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
>  1 file changed, 34 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 51640b710f..03b1e81634 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -2154,6 +2154,40 @@ (define-public python-pybedtools
>      ;; licensed lgpl2.1+
>      (license (list license:expat license:lgpl2.1+))))
>  
> +(define-public python-scDamAndTools
> +  (package
> +    (name "python-scDamAndTools")
> +    (version "1.0")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/KindLab/scDamAndTools";)
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +                "1mblw6cn5jqik6ky8cv7ry99z6jm1i4r71pzdfl398vrwbda65gd"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     (list #:tests? #f)) ;there are none
> +    (propagated-inputs (list python-h5py
> +                             python-numpy
> +                             python-sortedcontainers
> +                             python-pandas
> +                             python-pysam
> +                             python-tqdm))
> +    (native-inputs (list python-cython python-pytest))
> +    (home-page "https://github.com/KindLab/scDamAndTools";)
> +    (synopsis "Functions for processing raw scDam&T-seq data")
> +    (description
> +     "This is a set of unctions for processing raw scDam&T-seq data.
> +A method to simultaneously measure protein-DNA interactions and transcription
> +from single cells (Rooijers et al., 2019). scDam&T-seq combines a DamID-based
> +method to measure protein-DNA interactions and an adaptation of CEL-Seq to
> +measure transcription.  The starting point of the workflow is raw sequencing
> +data and the end result are tables of UMI-unique DamID and CEL-Seq counts.")
> +    (license license:expat)))
> +
>  (define-public python-bioframe
>    (package
>      (name "python-bioframe")
>
> base-commit: 1b2d43fe016848ea2ec16ff18cbc14340944fc4e
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add python-scDamAndTools.
>
>
>
>
> Date: 
>
> Mon, 28 Aug 2023 09:51:53 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.10.5; emacs 28.2
>
>
>
>
> Thanks for the patch.  I renamed it to all lowercase and changed the
> description a little bit.
>
> Pushed!
>
> -- 
> Ricardo
>
>
> --- End Message ---