From 8befd0940b4d443d5c2f1e91f9fe1b375f30fe1f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 13 Apr 2017 23:15:06 +0200
Subject: gnu: Add tadbit.

* gnu/packages/bioinformatics.scm (tadbit): New variable.
---
 gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b36d6bbdc..b47f136935 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9474,3 +9474,61 @@ applications for tackling some common problems in a user-friendly way.")
     ;; available under the GNU GPL (see the file COPYING.GPL).
     (license (list license:lgpl2.1+
                    license:gpl3+))))
+
+(define-public tadbit
+  (package
+    (name "tadbit")
+    (version "0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/3DGenomes/TADbit/"
+                                  "archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+    (build-system python-build-system)
+    (arguments
+     `(;; Tests are included and must be run after installation, but
+       ;; they are incomplete and thus cannot be run.
+       #:tests? #f
+       #:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-problems-with-setup.py
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; setup.py opens these files for writing
+             (chmod "_pytadbit/_version.py" #o664)
+             (chmod "README.rst" #o664)
+
+             ;; Don't attempt to install the bash completions to
+             ;; the home directory.
+             (rename-file "extras/.bash_completion"
+                          "extras/tadbit")
+             (substitute* "setup.py"
+               (("\\(path.expanduser\\('~'\\)")
+                (string-append "(\""
+                               (assoc-ref outputs "out")
+                               "/etc/bash_completion.d\""))
+               (("extras/\\.bash_completion")
+                "extras/tadbit"))
+             #t)))))
+    (inputs
+     ;; TODO: add Chimera for visualization
+     `(("imp" ,imp)
+       ("mcl" ,mcl)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-numpy" ,python2-numpy)
+       ("python2-matplotlib" ,python2-matplotlib)
+       ("python2-pysam" ,python2-pysam)))
+    (home-page "http://3dgenomes.github.io/TADbit/")
+    (synopsis "Analyze, model, and explore 3C-based data")
+    (description
+     "TADbit is a complete Python library to deal with all steps to analyze,
+model, and explore 3C-based data.  With TADbit the user can map FASTQ files to
+obtain raw interaction binned matrices (Hi-C like matrices), normalize and
+correct interaction matrices, identify adn compare the so-called
+@dfn{Topologically Associating Domains} (TADs), build 3D models from the
+interaction matrices, and finally, extract structural properties from the
+models.  TADbit is complemented by TADkit for visualizing 3D models.")
+    (license license:gpl3+)))
-- 
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