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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-10-02 16:37:03 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-03-01 11:51:24 +0100 |
| commit | d1e32822b4c70b2f0b545eabef62f75162354829 (patch) | |
| tree | af293334a9de60db99c336dcdbe8a502fcf11adb | |
| parent | d29150b55d4c0dcc371949d90d74b54d58bae098 (diff) | |
| download | patches-d1e32822b4c70b2f0b545eabef62f75162354829.tar patches-d1e32822b4c70b2f0b545eabef62f75162354829.tar.gz | |
gnu: Add PePr.
* gnu/packages/bioinformatics.scm (pepr): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eef33dd42f..78385af262 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+))) |