From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] Update deeptools. Date: Wed, 2 Mar 2016 20:50:05 -0500 Message-ID: <20160303015005.GA28589@jasmine> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46942) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1abIP3-0005d9-25 for guix-devel@gnu.org; Wed, 02 Mar 2016 20:50:11 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1abIOy-0003rN-Lg for guix-devel@gnu.org; Wed, 02 Mar 2016 20:50:09 -0500 Received: from out3-smtp.messagingengine.com ([66.111.4.27]:53781) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1abIOy-0003r9-Gu for guix-devel@gnu.org; Wed, 02 Mar 2016 20:50:04 -0500 Content-Disposition: inline In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ricardo Wurmus Cc: guix-devel 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 > 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 > 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 > 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 > 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 > 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 >