@@ 570,6 570,51 @@ resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public miso
+ (package
+ (name "miso")
+ (version "0.5.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://pypi.python.org/packages/source/m/misopy/misopy-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
+ (modules '((guix build utils)))
+ ;; use "gcc" instead of "cc" for compilation
+ (snippet
+ '(substitute* "setup.py"
+ (("^defines")
+ "cc.set_executables(
+compiler='gcc',
+compiler_so='gcc',
+linker_exe='gcc',
+linker_so='gcc -shared'); defines")))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; only Python 2 is supported
+ #:tests? #f)) ; no "test" target
+ (inputs
+ `(("samtools" ,samtools)
+ ("python-numpy" ,python2-numpy)
+ ("python-pysam" ,python2-pysam)
+ ("python-scipy" ,python2-scipy)
+ ("python-matplotlib" ,python2-matplotlib)))
+ (native-inputs
+ `(("python-setuptools" ,python2-setuptools)))
+ (home-page "http://genes.mit.edu/burgelab/miso/index.html")
+ (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
+ (description
+ "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
+the expression level of alternatively spliced genes from RNA-Seq data, and
+identifies differentially regulated isoforms or exons across samples. By
+modeling the generative process by which reads are produced from isoforms in
+RNA-Seq, the MISO model uses Bayesian inference to compute the probability
+that a read originated from a particular isoform.")
+ (license license:gpl2)))
+
(define-public rseqc
(package
(name "rseqc")