From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Add PePr.
Date: Fri, 23 Oct 2015 13:44:09 +0200 [thread overview]
Message-ID: <idjbnbpyfli.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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From 6aa9c0cb97350d5cccb43a78e69e2b8887347df0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 2 Oct 2015 16:37:03 +0200
Subject: [PATCH] gnu: Add PePr.
* gnu/packages/bioinformatics.scm (pepr): New variable.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d0bf38b..8a81150 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3054,3 +3054,41 @@ Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
identify genotyping errors, and to perform single-QTL and two-QTL,
two-dimensional genome scans.")
(license license:gpl3)))
+
+(define-public pepr
+ (package
+ (name "pepr")
+ (version "1.0.9")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://pypi.python.org/packages/source/P"
+ "/PePr/PePr-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; python2 only
+ #:tests? #f ; no tests included
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-egg
+ (lambda _
+ (substitute* "setup.py"
+ (("from setuptools import setup")
+ "from distutils.core import setup"))
+ #t)))))
+ (propagated-inputs
+ `(("python2-numpy" ,python2-numpy)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-pysam" ,python2-pysam)))
+ (home-page "http://github.com/fhcrc/seqmagick")
+ (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
+ (description
+ "PePr is a ChIP-Seq peak calling or differential binding analysis tool
+that is primarily designed for data with biological replicates. It uses a
+negative binomial distribution to model the read counts among the samples in
+the same group, and look for consistent differences between ChIP and control
+group or two ChIP groups run under different conditions. PePr was published
+on Bioinformatics on Jun 2014.")
+ (license license:gpl3+)))
--
2.1.0
next reply other threads:[~2015-10-23 11:44 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-10-23 11:44 Ricardo Wurmus [this message]
2015-10-26 14:40 ` [PATCH] Add PePr Ludovic Courtès
2016-03-01 10:51 ` Ricardo Wurmus
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