* [PATCH 0/3]: Add libyaml, pyyaml, pybedtools.
@ 2015-02-20 16:46 Ricardo Wurmus
2015-02-20 16:47 ` [PATCH 1/3]: Add libyaml Ricardo Wurmus
` (2 more replies)
0 siblings, 3 replies; 8+ messages in thread
From: Ricardo Wurmus @ 2015-02-20 16:46 UTC (permalink / raw)
To: Guix-devel
Attached is a series of patches adding libyaml, the Python bindings to
libyaml, and pybedtools (Python bindings to bedtools), which depends on
the former two.
~~ Ricardo
^ permalink raw reply [flat|nested] 8+ messages in thread* [PATCH 1/3]: Add libyaml 2015-02-20 16:46 [PATCH 0/3]: Add libyaml, pyyaml, pybedtools Ricardo Wurmus @ 2015-02-20 16:47 ` Ricardo Wurmus 2015-02-20 16:48 ` [PATCH 2/3]: Add pyyaml Ricardo Wurmus 2015-02-20 16:48 ` [PATCH 3/3]: Add pybedtools Ricardo Wurmus 2 siblings, 0 replies; 8+ messages in thread From: Ricardo Wurmus @ 2015-02-20 16:47 UTC (permalink / raw) To: Guix-devel [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #1: 0001-gnu-Add-libyaml.patch --] [-- Type: text/x-patch, Size: 1255 bytes --] From c52c742aaa90fb68e496ef83b1763125a514e606 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> Date: Fri, 20 Feb 2015 17:35:09 +0100 Subject: [PATCH 1/3] gnu: Add libyaml. * gnu/packages/web.scm (libyaml): New variable. --- gnu/packages/web.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 308434f..5296c43 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -799,3 +799,23 @@ select or poll.") server). It was primarily designed to be used by one person or a small group of people.") (license l:expat))) + +(define-public libyaml + (package + (name "libyaml") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (string-append + "http://pyyaml.org/download/libyaml/yaml-" + version ".tar.gz")) + (sha256 + (base32 + "1vrv5ly58bkmcyc049ad180f2m8iav6l9h3v8l2fqdmrny7yx1zs")))) + (build-system gnu-build-system) + (home-page "http://pyyaml.org/wiki/LibYAML") + (synopsis "YAML 1.1 parser and emitter written in C") + (description + "LibYAML is a YAML 1.1 parser and emitter written in C.") + (license l:expat))) -- 2.1.0 ^ permalink raw reply related [flat|nested] 8+ messages in thread
* [PATCH 2/3]: Add pyyaml. 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 ` Ricardo Wurmus 2015-02-20 17:58 ` Andreas Enge 2015-02-20 16:48 ` [PATCH 3/3]: Add pybedtools Ricardo Wurmus 2 siblings, 1 reply; 8+ messages in thread From: Ricardo Wurmus @ 2015-02-20 16:48 UTC (permalink / raw) To: Guix-devel [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #1: 0002-gnu-Add-pyyaml.patch --] [-- Type: text/x-patch, Size: 2120 bytes --] From 4b8d6f7a10bc4c20c267a4c26be4e5678ce96382 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 2/3] 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 cb25419..e19d707 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) @@ -1730,6 +1731,37 @@ 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) + (propagated-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 ^ permalink raw reply related [flat|nested] 8+ messages in thread
* Re: [PATCH 2/3]: Add pyyaml. 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 0 siblings, 1 reply; 8+ messages in thread From: Andreas Enge @ 2015-02-20 17:58 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: Guix-devel 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? > + (description > + " PyYAML is a YAML parser and emitter for Python. PyYAML features a ↑ a space too much Andreas ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: [PATCH 2/3]: Add pyyaml. 2015-02-20 17:58 ` Andreas Enge @ 2015-02-26 13:40 ` Ricardo Wurmus 2015-02-26 14:15 ` Ricardo Wurmus 2015-02-28 14:21 ` Andreas Enge 0 siblings, 2 replies; 8+ messages in thread From: Ricardo Wurmus @ 2015-02-26 13:40 UTC (permalink / raw) To: Andreas Enge; +Cc: Guix-devel [-- Attachment #1: Type: text/plain, Size: 539 bytes --] 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 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-gnu-Add-pyyaml.patch --] [-- Type: text/x-patch, Size: 2109 bytes --] 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 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #3: 0002-gnu-Add-pybedtools.patch --] [-- Type: text/x-patch, Size: 2316 bytes --] 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 ^ permalink raw reply related [flat|nested] 8+ messages in thread
* Re: [PATCH 2/3]: Add pyyaml. 2015-02-26 13:40 ` Ricardo Wurmus @ 2015-02-26 14:15 ` Ricardo Wurmus 2015-02-28 14:21 ` Andreas Enge 1 sibling, 0 replies; 8+ messages in thread From: Ricardo Wurmus @ 2015-02-26 14:15 UTC (permalink / raw) To: Andreas Enge; +Cc: Guix-devel Ricardo Wurmus writes: > Attached are new patches for pyyaml and pybedtools (libyaml has already > been pushed). Please ignore the + #:use-module (gnu packages web) in the pybedtools patch. It's not actually needed and slipped into this patch set by accident. ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: [PATCH 2/3]: Add pyyaml. 2015-02-26 13:40 ` Ricardo Wurmus 2015-02-26 14:15 ` Ricardo Wurmus @ 2015-02-28 14:21 ` Andreas Enge 1 sibling, 0 replies; 8+ messages in thread From: Andreas Enge @ 2015-02-28 14:21 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: Guix-devel Hello, On Thu, Feb 26, 2015 at 02:40:05PM +0100, Ricardo Wurmus wrote: > * gnu/packages/python.scm (python-pyyaml, python2-pyyaml): New variables. this looks good, please push. > * gnu/packages/bioinformatics.scm (python2-pybedtools): New variable. > + (synopsis "Python wrapper for BEDtools programs") This sounds as if the result is a python stand-alone program and not a library? In the first case, it should be called "pybedtools". Otherwise okay to push. Andreas ^ permalink raw reply [flat|nested] 8+ messages in thread
* [PATCH 3/3]: Add pybedtools. 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 16:48 ` Ricardo Wurmus 2 siblings, 0 replies; 8+ messages in thread From: Ricardo Wurmus @ 2015-02-20 16:48 UTC (permalink / raw) To: Guix-devel [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #1: 0003-gnu-Add-pybedtools.patch --] [-- Type: text/x-patch, Size: 2315 bytes --] From 26054dc29fa3132e58b2a71e20f37cfc3446a68d 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 3/3] 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..092a6e3 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) + ("python-setuptools" ,python2-setuptools))) + (propagated-inputs + `(("bedtools" ,bedtools) + ("samtools" ,samtools))) + (native-inputs + `(("python-pyyaml" ,python2-pyyaml) + ("python-nose" ,python2-nose))) + (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 ^ permalink raw reply related [flat|nested] 8+ messages in thread
end of thread, other threads:[~2015-02-28 14:22 UTC | newest] Thread overview: 8+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 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 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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