[PATCH 0/3]: Add libyaml, pyyaml, pybedtools.

[PATCH 0/3]: Add libyaml, pyyaml, pybedtools.

[Ricardo Wurmus]

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

[PATCH 1/3]: Add libyaml

[Ricardo Wurmus]

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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

[PATCH 2/3]: Add pyyaml.

[Ricardo Wurmus]

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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

[PATCH 3/3]: Add pybedtools.

[Ricardo Wurmus]

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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

Re: [PATCH 2/3]: Add pyyaml.

[Andreas Enge]

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

Re: [PATCH 2/3]: Add pyyaml.

[Ricardo Wurmus]

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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

Re: [PATCH 2/3]: Add pyyaml.

[Ricardo Wurmus]

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.

Re: [PATCH 2/3]: Add pyyaml.

[Andreas Enge]

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