@@ 4483,3 4483,44 @@ 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
+ ;; When setuptools is used a ".egg" archive is generated and
+ ;; installed. This makes it hard to actually run PePr. This issue
+ ;; has been reported upstream:
+ ;; https://github.com/shawnzhangyx/PePr/issues/9
+ (add-after 'unpack 'disable-egg-generation
+ (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 "https://code.google.com/p/pepr-chip-seq/")
+ (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.")
+ (license license:gpl3+)))