From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Guix-devel <guix-devel@gnu.org>
Subject: [PATCH 3/3]: Add pybedtools.
Date: Fri, 20 Feb 2015 17:48:35 +0100 [thread overview]
Message-ID: <idjegpkil5o.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <idjioewil9f.fsf@bimsb-sys02.mdc-berlin.net>
[-- 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
prev parent reply other threads:[~2015-02-20 16:48 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
2015-02-26 14:15 ` Ricardo Wurmus
2015-02-28 14:21 ` Andreas Enge
2015-02-20 16:48 ` Ricardo Wurmus [this message]
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=idjegpkil5o.fsf@bimsb-sys02.mdc-berlin.net \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.