Re: [PATCH] Add python–plastid, python-twobitreader.

[Leo Famulari <leo@famulari.name>]

On Wed, Apr 06, 2016 at 04:36:52PM +0200, Ricardo Wurmus wrote:
> From ecb23f8eb2dbd83cbaa97972d6258ccb44c58194 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 6 Apr 2016 16:34:19 +0200
> Subject: [PATCH 1/2] gnu: Add python-twobitreader.
> 
> * gnu/packages/bioinformatics.scm (python-twobitreader,
>   python2-twobitreader): New variables.

LGTM!

> ---
>  gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
>  1 file changed, 23 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 01e9060..d13303d 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1038,6 +1038,29 @@ also includes an interface for tabix.")
>  (define-public python2-pysam
>    (package-with-python2 python-pysam))
>  
> +(define-public python-twobitreader
> +  (package
> +    (name "python-twobitreader")
> +    (version "3.1.2")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (pypi-uri "twobitreader" version))
> +              (sha256
> +               (base32
> +                "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
> +    (build-system python-build-system)
> +    (native-inputs
> +     `(("python-sphinx" ,python-sphinx)))
> +    (home-page "https://github.com/benjschiller/twobitreader")
> +    (synopsis "Python library for reading .2bit files")
> +    (description
> +     "twobitreader is a Python library for reading .2bit files as used by the
> +UCSC genome browser.")
> +    (license license:artistic2.0)))
> +
> +(define-public python2-twobitreader
> +  (package-with-python2 python-twobitreader))
> +
>  (define-public cd-hit
>    (package
>      (name "cd-hit")
> -- 
> 2.1.0
> 

> From a2604f6d4b03727ebd7922ce373486b13ab31c00 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 6 Apr 2016 16:35:09 +0200
> Subject: [PATCH 2/2] gnu: Add python-plastid.
> 
> * gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
>   variables.
> ---
>  gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
>  1 file changed, 35 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index d13303d..1896002 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1061,6 +1061,41 @@ UCSC genome browser.")
>  (define-public python2-twobitreader
>    (package-with-python2 python-twobitreader))
>  
> +(define-public python-plastid
> +  (package
> +    (name "python-plastid")
> +    (version "0.4.5")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (pypi-uri "plastid" version))
> +              (sha256
> +               (base32
> +                "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
> +    (build-system python-build-system)
> +    (arguments
> +     ;; Some test files are not included.
> +     `(#:tests? #f))
> +    (propagated-inputs
> +     `(("python-numpy" ,python-numpy)
> +       ("python-scipy" ,python-scipy)
> +       ("python-pandas" ,python-pandas)
> +       ("python-pysam" ,python-pysam)
> +       ("python-matplotlib" ,python-matplotlib)
> +       ("python-biopython" ,python-biopython)
> +       ("python-twobitreader" ,python-twobitreader)))
> +    (native-inputs
> +     `(("python-cython" ,python-cython)
> +       ("python-nose" ,python-nose)))
> +    (home-page "https://github.com/joshuagryphon/plastid")
> +    (synopsis "Python library for genomic analysis")
> +    (description
> +     "plastid is a Python library for genomic analysis – in particular,
> +high-throughput sequencing data – with an emphasis on simplicity.")
> +    (license license:bsd-3)))
> +
> +(define-public python2-plastid
> +  (package-with-python2 python-plastid))
> +
>  (define-public cd-hit
>    (package
>      (name "cd-hit")
> -- 
> 2.1.0
>