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authorRicardo Wurmus <rekado@elephly.net>2017-04-13 23:15:06 +0200
committerRicardo Wurmus <rekado@elephly.net>2017-06-09 03:32:23 +0200
commit8befd0940b4d443d5c2f1e91f9fe1b375f30fe1f (patch)
treee6b5dc3d517ab4f3fa2038375ae4d334b8c365a4
parentaa163424b249bb11525fccc0a87cf60aa687ac60 (diff)
downloadguix-8befd0940b4d443d5c2f1e91f9fe1b375f30fe1f.tar
guix-8befd0940b4d443d5c2f1e91f9fe1b375f30fe1f.tar.gz
gnu: Add tadbit.
* gnu/packages/bioinformatics.scm (tadbit): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm58
1 files changed, 58 insertions, 0 deletions
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+)))