From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH 2/3]: Add pyyaml. Date: Thu, 26 Feb 2015 14:40:05 +0100 Message-ID: References: <20150220175836.GB15485@debian.math.u-bordeaux1.fr> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59272) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YQyfr-0007VQ-Oh for guix-devel@gnu.org; Thu, 26 Feb 2015 08:40:21 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YQyfm-0003nq-O8 for guix-devel@gnu.org; Thu, 26 Feb 2015 08:40:19 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:34431) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YQyfm-0003nh-BR for guix-devel@gnu.org; Thu, 26 Feb 2015 08:40:14 -0500 In-Reply-To: <20150220175836.GB15485@debian.math.u-bordeaux1.fr> 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: Andreas Enge Cc: Guix-devel --=-=-= Content-Type: text/plain Andreas Enge writes: > On Fri, Feb 20, 2015 at 05:48:04PM +0100, Ricardo Wurmus wrote: >> + (propagated-inputs >> + `(("libyaml" ,libyaml))) > > Is it really needed to propagate the input? The _yaml.cpython-33m.so library > is automatically linked with libyaml-0.so.2 thanks to our ld. If it is needed, > could you add a quick explanation? Checked again without propagating the input and it does work. Thanks for catching this. Attached are new patches for pyyaml and pybedtools (libyaml has already been pushed). ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-pyyaml.patch" >From 53cafc191324589d760746b1e32276173e169c6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Feb 2015 17:38:17 +0100 Subject: [PATCH 1/2] gnu: Add pyyaml. * gnu/packages/python.scm (python-pyyaml, python2-pyyaml): New variables. --- gnu/packages/python.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bbff241..087f9e6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -53,6 +53,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages texlive) #:use-module (gnu packages texinfo) + #:use-module (gnu packages web) #:use-module (gnu packages which) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) @@ -1722,6 +1723,37 @@ environments and back.") (define-public python2-itsdangerous (package-with-python2 python-itsdangerous)) +(define-public python-pyyaml + (package + (name "python-pyyaml") + (version "3.11") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/P/PyYAML/PyYAML-" + version ".tar.gz")) + (sha256 + (base32 + "1s26125vfnskng58ym37xhwv8v0mm95b2cwbjfag8prfhy596v63")))) + (build-system python-build-system) + (inputs + `(("libyaml" ,libyaml))) + (native-inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "http://pyyaml.org/wiki/PyYAML") + (synopsis "YAML parser and emitter for Python") + (description + "PyYAML is a YAML parser and emitter for Python. PyYAML features a +complete YAML 1.1 parser, Unicode support, pickle support, capable extension +API, and sensible error messages. PyYAML supports standard YAML tags and +provides Python-specific tags that allow to represent an arbitrary Python +object.") + (license license:expat))) + +(define-public python2-pyyaml + (package-with-python2 python-pyyaml)) + (define-public python-virtualenv (package (name "python-virtualenv") -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-Add-pybedtools.patch" >From 014e5525e4676b5bfbca41ba5f99ba0cec5a026c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Feb 2015 17:43:08 +0100 Subject: [PATCH 2/2] gnu: Add pybedtools. * gnu/packages/bioinformatics.scm (python2-pybedtools): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b64dab7..a425f61 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -33,6 +33,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages tbb) #:use-module (gnu packages vim) + #:use-module (gnu packages web) #:use-module (gnu packages zip)) (define-public bedops @@ -141,6 +142,39 @@ intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.") (license license:gpl2))) +(define-public python2-pybedtools + (package + (name "python2-pybedtools") + (version "0.6.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" + version ".tar.gz")) + (sha256 + (base32 + "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; no Python 3 support + (inputs + `(("python-cython" ,python2-cython) + ("python-matplotlib" ,python2-matplotlib))) + (propagated-inputs + `(("bedtools" ,bedtools) + ("samtools" ,samtools))) + (native-inputs + `(("python-pyyaml" ,python2-pyyaml) + ("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "https://pythonhosted.org/pybedtools/") + (synopsis "Python wrapper for BEDtools programs") + (description + "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, +which are widely used for genomic interval manipulation or \"genome algebra\". +pybedtools extends BEDTools by offering feature-level manipulations from with +Python.") + (license license:gpl2+))) + (define-public bowtie (package (name "bowtie") -- 2.1.0 --=-=-=--