From: Leo Famulari <leo@famulari.name>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH] Update deeptools.
Date: Wed, 2 Mar 2016 20:50:05 -0500 [thread overview]
Message-ID: <20160303015005.GA28589@jasmine> (raw)
In-Reply-To: <idjegbv1vdz.fsf@bimsb-sys02.mdc-berlin.net>
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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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
>
next prev parent reply other threads:[~2016-03-03 1:50 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-02-29 13:47 [PATCH] Update deeptools Ricardo Wurmus
2016-03-03 1:50 ` Leo Famulari [this message]
2016-03-03 12:32 ` Ricardo Wurmus
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20160303015005.GA28589@jasmine \
--to=leo@famulari.name \
--cc=guix-devel@gnu.org \
--cc=ricardo.wurmus@mdc-berlin.de \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.