gnu: Add MISO.

* gnu/packages/bioinformatics.scm (miso): New variable.
This commit is contained in:
Ricardo Wurmus 2015-03-13 10:31:49 +01:00
parent 9a8336d87b
commit ddd82e0e76

View file

@ -570,6 +570,51 @@ (define-public macs
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")