Re: [PATCH] Update deeptools.

[Leo Famulari]

On Mon, Feb 29, 2016 at 02:47:04PM +0100, Ricardo Wurmus wrote:
> Hi Guix,
> 
> the goal of this series of patches is to update deeptools.
> 
> First I moved the “*-pysam” packages from python.scm to
> bioinformatics.scm, then updated them.  Then added “pybigwig”, cleaned
> up “deeptools” (used “propagated-inputs” for no good reason), and
> finally updated the package.

All look good, although can you say if pysam needs setuptools at
run-time? Or does it make sense to change it to a native-input?

> 
> ~~ Ricardo
> 

> From f960fda0d38d0a71519072ad8fae8edd7b90b2c6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> Date: Thu, 25 Feb 2016 14:01:14 +0100
> Subject: [PATCH 1/5] gnu: python-pysam, python2-pysam: Move to
>  bioinformatics.scm.
> 
> * gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
> * gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
>   ...here.
> ---
>  gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
>  gnu/packages/python.scm         | 38 --------------------------------------
>  2 files changed, 38 insertions(+), 38 deletions(-)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index e570487..a86f7d6 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -808,6 +808,44 @@ and more accurate.  BWA-MEM also has better performance 
> than BWA-backtrack for
>  multiple sequence alignments.")
>      (license license:expat)))
>  
> +(define-public python-pysam
> +  (package
> +    (name "python-pysam")
> +    (version "0.8.1")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append 
> "https://pypi.python.org/packages/source/p/pysam/pysam-";
> +                           version ".tar.gz"))
> +       (sha256
> +        (base32
> +         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:tests? #f ; tests are excluded in the manifest
> +       #:phases
> +       (alist-cons-before
> +        'build 'set-flags
> +        (lambda _
> +          (setenv "LDFLAGS" "-lncurses")
> +          (setenv "CFLAGS" "-D_CURSES_LIB=1"))
> +        %standard-phases)))
> +    (inputs
> +     `(("python-cython"     ,python-cython)
> +       ("python-setuptools" ,python-setuptools)
> +       ("ncurses"           ,ncurses)
> +       ("zlib"              ,zlib)))
> +    (home-page "https://github.com/pysam-developers/pysam";)
> +    (synopsis "Python bindings to the SAMtools C API")
> +    (description
> +     "Pysam is a Python module for reading and manipulating files in the
> +SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
> +also includes an interface for tabix.")
> +    (license license:expat)))
> +
> +(define-public python2-pysam
> +  (package-with-python2 python-pysam))
> +
>  (define-public clipper
>    (package
>      (name "clipper")
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index 46eda76..214a8ea 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -1039,44 +1039,6 @@ get the local timezone information, unless you know 
> the zoneinfo name, and
>  under several distributions that's hard or impossible to figure out.")
>      (license cc0)))
>  
> -(define-public python-pysam
> -  (package
> -    (name "python-pysam")
> -    (version "0.8.1")
> -    (source
> -     (origin
> -       (method url-fetch)
> -       (uri (string-append 
> "https://pypi.python.org/packages/source/p/pysam/pysam-";
> -                           version ".tar.gz"))
> -       (sha256
> -        (base32
> -         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
> -    (build-system python-build-system)
> -    (arguments
> -     `(#:tests? #f ; tests are excluded in the manifest
> -       #:phases
> -       (alist-cons-before
> -        'build 'set-flags
> -        (lambda _
> -          (setenv "LDFLAGS" "-lncurses")
> -          (setenv "CFLAGS" "-D_CURSES_LIB=1"))
> -        %standard-phases)))
> -    (inputs
> -     `(("python-cython"     ,python-cython)
> -       ("python-setuptools" ,python-setuptools)
> -       ("ncurses"           ,ncurses)
> -       ("zlib"              ,zlib)))
> -    (home-page "https://github.com/pysam-developers/pysam";)
> -    (synopsis "Python bindings to the SAMtools C API")
> -    (description
> -     "Pysam is a Python module for reading and manipulating files in the
> -SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
> -also includes an interface for tabix.")
> -    (license license:expat)))
> -
> -(define-public python2-pysam
> -  (package-with-python2 python-pysam))
> -
>  (define-public python2-pysqlite
>    (package
>      (name "python2-pysqlite")
> -- 
> 2.1.0
> 

> From 473a6f8b1e56984b308533a9baa44979c6450e7d Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> Date: Mon, 29 Feb 2016 14:36:25 +0100
> Subject: [PATCH 2/5] gnu: python-pysam: Update to 0.8.4.
> 
> * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
> ---
>  gnu/packages/bioinformatics.scm | 16 +++++++---------
>  1 file changed, 7 insertions(+), 9 deletions(-)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index a86f7d6..28754dc 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -811,15 +811,13 @@ multiple sequence alignments.")
>  (define-public python-pysam
>    (package
>      (name "python-pysam")
> -    (version "0.8.1")
> -    (source
> -     (origin
> -       (method url-fetch)
> -       (uri (string-append 
> "https://pypi.python.org/packages/source/p/pysam/pysam-";
> -                           version ".tar.gz"))
> -       (sha256
> -        (base32
> -         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
> +    (version "0.8.4")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (pypi-uri "pysam" version))
> +              (sha256
> +               (base32
> +                "1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh"))))
>      (build-system python-build-system)
>      (arguments
>       `(#:tests? #f ; tests are excluded in the manifest
> -- 
> 2.1.0
> 

> From 1d58bb0aa9894295f6f949d463bcdfa54b4d2980 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> Date: Mon, 29 Feb 2016 14:37:38 +0100
> Subject: [PATCH 3/5] gnu: Add python-pybigwig.
> 
> * gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
>   New variables.
> ---
>  gnu/packages/bioinformatics.scm | 41 
> +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 41 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 28754dc..d7aae6e 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1164,6 +1164,47 @@ other types of unwanted sequence from high-throughput 
> sequencing reads.")
>  files.")
>      (license license:expat)))
>  
> +(define-public python-pybigwig
> +  (package
> +    (name "python-pybigwig")
> +    (version "0.2.5")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (pypi-uri "pyBigWig" version))
> +              (sha256
> +               (base32
> +                "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               '(begin
> +                  ;; Delete bundled libBigWig sources
> +                  (delete-file-recursively "libBigWig")))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'link-with-libBigWig
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (substitute* "setup.py"
> +               (("libs=\\[") "libs=[\"BigWig\", "))
> +             #t)))))
> +    (inputs
> +     `(("libbigwig" ,libbigwig)
> +       ("zlib" ,zlib)
> +       ("curl" ,curl)))
> +    (home-page "https://github.com/dpryan79/pyBigWig";)
> +    (synopsis "Access bigWig files in Python using libBigWig")
> +    (description
> +     "This package provides Python bindings to the libBigWig library for
> +accessing bigWig files.")
> +    (license license:expat)))
> +
> +(define-public python2-pybigwig
> +  (let ((pybigwig (package-with-python2 python-pybigwig)))
> +    (package (inherit pybigwig)
> +      (native-inputs
> +       `(("python-setuptools" ,python2-setuptools))))))
> +
>  (define-public deeptools
>    (package
>      (name "deeptools")
> -- 
> 2.1.0
> 

> From 37837afefee0df1459322b04b1e26257539b8d02 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> Date: Mon, 29 Feb 2016 14:38:57 +0100
> Subject: [PATCH 4/5] gnu: deeptools: Change "propagated-inputs" to "inputs".
> 
> * gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
> all inputs from here...
> [inputs]: ...to here.
> ---
>  gnu/packages/bioinformatics.scm | 2 +-
>  1 file changed, 1 insertion(+), 1 deletion(-)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index d7aae6e..472219e 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1221,7 +1221,7 @@ accessing bigWig files.")
>      (build-system python-build-system)
>      (arguments
>       `(#:python ,python-2))
> -    (propagated-inputs
> +    (inputs
>       `(("python-scipy" ,python2-scipy)
>         ("python-numpy" ,python2-numpy)
>         ("python-matplotlib" ,python2-matplotlib)
> -- 
> 2.1.0
> 

> From 197ebd69cc27de3c724d3e01e6c08f843b8b3f07 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> Date: Mon, 29 Feb 2016 14:40:10 +0100
> Subject: [PATCH 5/5] gnu: deeptools: Update to 2.1.1.
> 
> * gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
> [inputs]: Add "python2-numpydoc" and "python2-pybigwig".
> ---
>  gnu/packages/bioinformatics.scm | 13 +++++++------
>  1 file changed, 7 insertions(+), 6 deletions(-)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 472219e..6df7d5c 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1208,25 +1208,26 @@ accessing bigWig files.")
>  (define-public deeptools
>    (package
>      (name "deeptools")
> -    (version "1.5.11")
> +    (version "2.1.1")
>      (source (origin
>                (method url-fetch)
> -              (uri (string-append
> -                    "https://github.com/fidelram/deepTools/archive/";
> -                    version ".tar.gz"))
> +              (uri (string-append "https://github.com/fidelram/deepTools/";
> +                                  "archive/" version ".tar.gz"))
>                (file-name (string-append name "-" version ".tar.gz"))
>                (sha256
>                 (base32
> -                "1kaagygcbvjs9sxd9cqmskd02wcfp9imvb735r087w7hwqpvz6fs"))))
> +                "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
>      (build-system python-build-system)
>      (arguments
>       `(#:python ,python-2))
>      (inputs
>       `(("python-scipy" ,python2-scipy)
>         ("python-numpy" ,python2-numpy)
> +       ("python-numpydoc" ,python2-numpydoc)
>         ("python-matplotlib" ,python2-matplotlib)
>         ("python-bx-python" ,python2-bx-python)
> -       ("python-pysam" ,python2-pysam)))
> +       ("python-pysam" ,python2-pysam)
> +       ("python-pybigwig" ,python2-pybigwig)))
>      (native-inputs
>       `(("python-mock" ,python2-mock) ;for tests
>         ("python-pytz" ,python2-pytz) ;for tests
> -- 
> 2.1.0
>