From: Ricardo Wurmus <rekado@elephly.net>
To: 27175@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: bug#27175: [PATCH 6/6] gnu: Add tadbit.
Date: Wed, 31 May 2017 23:16:11 +0200 [thread overview]
Message-ID: <20170531211611.14094-6-rekado@elephly.net> (raw)
In-Reply-To: <20170531211611.14094-1-rekado@elephly.net>
* gnu/packages/bioinformatics.scm (tadbit): New variable.
---
gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa5c32a54..323a2ee94 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9436,3 +9436,63 @@ 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)))))
+ ;; (native-inputs
+ ;; `(("python2-setuptools" ,python2-setuptools)))
+ (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+)))
--
2.12.2
next prev parent reply other threads:[~2017-05-31 21:17 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-05-31 21:11 bug#27175: Some bioinfo tools Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 1/6] gnu: Add ritornello Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 2/6] gnu: Add trim-galore Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 3/6] gnu: Add gess Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 4/6] gnu: Add phylip Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 5/6] gnu: Add imp Ricardo Wurmus
2017-05-31 21:16 ` Ricardo Wurmus [this message]
2017-06-02 16:41 ` bug#27175: [PATCH 6/6] gnu: Add tadbit Leo Famulari
2017-06-09 1:33 ` Ricardo Wurmus
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