From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Andreas Enge <andreas@enge.fr>
Cc: Guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH 2/3]: Add pyyaml.
Date: Thu, 26 Feb 2015 14:40:05 +0100 [thread overview]
Message-ID: <idja900hjuy.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <20150220175836.GB15485@debian.math.u-bordeaux1.fr>
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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
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From 53cafc191324589d760746b1e32276173e169c6a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
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From 014e5525e4676b5bfbca41ba5f99ba0cec5a026c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
next prev parent reply other threads:[~2015-02-26 13:40 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-02-20 16:46 [PATCH 0/3]: Add libyaml, pyyaml, pybedtools Ricardo Wurmus
2015-02-20 16:47 ` [PATCH 1/3]: Add libyaml Ricardo Wurmus
2015-02-20 16:48 ` [PATCH 2/3]: Add pyyaml Ricardo Wurmus
2015-02-20 17:58 ` Andreas Enge
2015-02-26 13:40 ` Ricardo Wurmus [this message]
2015-02-26 14:15 ` Ricardo Wurmus
2015-02-28 14:21 ` Andreas Enge
2015-02-20 16:48 ` [PATCH 3/3]: Add pybedtools Ricardo Wurmus
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