* [PATCH] Add python–plastid, python-twobitreader.
@ 2016-04-06 14:36 Ricardo Wurmus
2016-04-06 19:11 ` Leo Famulari
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2016-04-06 14:36 UTC (permalink / raw)
To: guix-devel
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-Add-python-twobitreader.patch --]
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From ecb23f8eb2dbd83cbaa97972d6258ccb44c58194 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 6 Apr 2016 16:34:19 +0200
Subject: [PATCH 1/2] gnu: Add python-twobitreader.
* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader): New variables.
---
gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 01e9060..d13303d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1038,6 +1038,29 @@ also includes an interface for tabix.")
(define-public python2-pysam
(package-with-python2 python-pysam))
+(define-public python-twobitreader
+ (package
+ (name "python-twobitreader")
+ (version "3.1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "twobitreader" version))
+ (sha256
+ (base32
+ "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-sphinx" ,python-sphinx)))
+ (home-page "https://github.com/benjschiller/twobitreader")
+ (synopsis "Python library for reading .2bit files")
+ (description
+ "twobitreader is a Python library for reading .2bit files as used by the
+UCSC genome browser.")
+ (license license:artistic2.0)))
+
+(define-public python2-twobitreader
+ (package-with-python2 python-twobitreader))
+
(define-public cd-hit
(package
(name "cd-hit")
--
2.1.0
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From a2604f6d4b03727ebd7922ce373486b13ab31c00 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 6 Apr 2016 16:35:09 +0200
Subject: [PATCH 2/2] gnu: Add python-plastid.
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
variables.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d13303d..1896002 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1061,6 +1061,41 @@ UCSC genome browser.")
(define-public python2-twobitreader
(package-with-python2 python-twobitreader))
+(define-public python-plastid
+ (package
+ (name "python-plastid")
+ (version "0.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "plastid" version))
+ (sha256
+ (base32
+ "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
+ (build-system python-build-system)
+ (arguments
+ ;; Some test files are not included.
+ `(#:tests? #f))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)
+ ("python-pandas" ,python-pandas)
+ ("python-pysam" ,python-pysam)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-biopython" ,python-biopython)
+ ("python-twobitreader" ,python-twobitreader)))
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-nose" ,python-nose)))
+ (home-page "https://github.com/joshuagryphon/plastid")
+ (synopsis "Python library for genomic analysis")
+ (description
+ "plastid is a Python library for genomic analysis – in particular,
+high-throughput sequencing data – with an emphasis on simplicity.")
+ (license license:bsd-3)))
+
+(define-public python2-plastid
+ (package-with-python2 python-plastid))
+
(define-public cd-hit
(package
(name "cd-hit")
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add python–plastid, python-twobitreader.
2016-04-06 14:36 [PATCH] Add python–plastid, python-twobitreader Ricardo Wurmus
@ 2016-04-06 19:11 ` Leo Famulari
0 siblings, 0 replies; 2+ messages in thread
From: Leo Famulari @ 2016-04-06 19:11 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
On Wed, Apr 06, 2016 at 04:36:52PM +0200, Ricardo Wurmus wrote:
> From ecb23f8eb2dbd83cbaa97972d6258ccb44c58194 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 6 Apr 2016 16:34:19 +0200
> Subject: [PATCH 1/2] gnu: Add python-twobitreader.
>
> * gnu/packages/bioinformatics.scm (python-twobitreader,
> python2-twobitreader): New variables.
LGTM!
> ---
> gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
> 1 file changed, 23 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 01e9060..d13303d 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1038,6 +1038,29 @@ also includes an interface for tabix.")
> (define-public python2-pysam
> (package-with-python2 python-pysam))
>
> +(define-public python-twobitreader
> + (package
> + (name "python-twobitreader")
> + (version "3.1.2")
> + (source (origin
> + (method url-fetch)
> + (uri (pypi-uri "twobitreader" version))
> + (sha256
> + (base32
> + "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
> + (build-system python-build-system)
> + (native-inputs
> + `(("python-sphinx" ,python-sphinx)))
> + (home-page "https://github.com/benjschiller/twobitreader")
> + (synopsis "Python library for reading .2bit files")
> + (description
> + "twobitreader is a Python library for reading .2bit files as used by the
> +UCSC genome browser.")
> + (license license:artistic2.0)))
> +
> +(define-public python2-twobitreader
> + (package-with-python2 python-twobitreader))
> +
> (define-public cd-hit
> (package
> (name "cd-hit")
> --
> 2.1.0
>
> From a2604f6d4b03727ebd7922ce373486b13ab31c00 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 6 Apr 2016 16:35:09 +0200
> Subject: [PATCH 2/2] gnu: Add python-plastid.
>
> * gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
> variables.
> ---
> gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
> 1 file changed, 35 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index d13303d..1896002 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1061,6 +1061,41 @@ UCSC genome browser.")
> (define-public python2-twobitreader
> (package-with-python2 python-twobitreader))
>
> +(define-public python-plastid
> + (package
> + (name "python-plastid")
> + (version "0.4.5")
> + (source (origin
> + (method url-fetch)
> + (uri (pypi-uri "plastid" version))
> + (sha256
> + (base32
> + "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
> + (build-system python-build-system)
> + (arguments
> + ;; Some test files are not included.
> + `(#:tests? #f))
> + (propagated-inputs
> + `(("python-numpy" ,python-numpy)
> + ("python-scipy" ,python-scipy)
> + ("python-pandas" ,python-pandas)
> + ("python-pysam" ,python-pysam)
> + ("python-matplotlib" ,python-matplotlib)
> + ("python-biopython" ,python-biopython)
> + ("python-twobitreader" ,python-twobitreader)))
> + (native-inputs
> + `(("python-cython" ,python-cython)
> + ("python-nose" ,python-nose)))
> + (home-page "https://github.com/joshuagryphon/plastid")
> + (synopsis "Python library for genomic analysis")
> + (description
> + "plastid is a Python library for genomic analysis – in particular,
> +high-throughput sequencing data – with an emphasis on simplicity.")
> + (license license:bsd-3)))
> +
> +(define-public python2-plastid
> + (package-with-python2 python-plastid))
> +
> (define-public cd-hit
> (package
> (name "cd-hit")
> --
> 2.1.0
>
^ permalink raw reply [flat|nested] 2+ messages in thread
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2016-04-06 14:36 [PATCH] Add python–plastid, python-twobitreader Ricardo Wurmus
2016-04-06 19:11 ` Leo Famulari
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