bug#64992: closed ([PATCH] gnu: Add python-baltica.)

[GNU bug Tracking System]

Your message dated Wed, 02 Aug 2023 08:48:37 +0200
with message-id <87a5va7xcu.fsf@elephly.net>
and subject line [PATCH] gnu: Add python-baltica.
has caused the debbugs.gnu.org bug report #64992,
regarding [PATCH] gnu: Add python-baltica.
to be marked as done.

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-- 
64992: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=64992
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add python-baltica.
>
>
>
>
> Date: 
>
> Tue, 1 Aug 2023 13:46:37 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (python-baltica): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
>  1 file changed, 43 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 6080c899af..6d745262b3 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5056,6 +5056,49 @@ (define-public edirect-go-programs
>             go-golang-org-x-image
>             go-golang-org-x-text))))
>  
> +(define-public python-baltica
> +  (package
> +    (name "python-baltica")
> +    (version "1.1.2")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/dieterich-lab/Baltica";)
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +                "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     (list #:phases '(modify-phases %standard-phases
> +                       (replace 'check
> +                         (lambda _
> +                           ;; The tests need to be run from elsewhere...
> +                           (mkdir-p "/tmp/test")
> +                           (copy-recursively ".tests" "/tmp/test")
> +                           (with-directory-excursion "/tmp/test"
> +                             (invoke "pytest" "-v" "--doctest-modules")))))))
> +    (propagated-inputs (list python-anndata
> +                             python-click
> +                             python-flask
> +                             python-flask-wtf
> +                             gunicorn
> +                             python-h5py
> +                             python-pysam
> +                             python-numpy
> +                             python-psutil
> +                             python-pyyaml
> +                             python-scipy
> +                             snakemake-7))
> +    (native-inputs (list python-pytest python-pyfakefs python-cython))
> +    (home-page "https://github.com/dieterich-lab/Baltica";)
> +    (synopsis "Integrated splice junction usage analysis")
> +    (description
> +     "This framework facilitates the execution of differential junction usage 
> methods.
> +Additionally, it enables the integration of results from multiple DJU 
> methods.")
> +    (license license:expat)))
> +
>  (define-public python-bamnostic
>    (package
>      (name "python-bamnostic")
>
> base-commit: 34b56974dfe720e5e30f04409ac216747d7e3f5c
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add python-baltica.
>
>
>
>
> Date: 
>
> Wed, 02 Aug 2023 08:48:37 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.10.5; emacs 28.2
>
>
>
>
> Pushed with commit 5a293d0830aa9369e388d37fe767d5bf98af01b7.  Thanks for
> the patch!
>
> -- 
> Ricardo
>
>
> --- End Message ---