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gnu: miso: Update to 0.5.4-1.b714021.

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* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021.
[source]: Fetch via git; simplify snippet.
[inputs]: Replace samtools with samtools-1.2.
[home-page]: Update to new location.
This commit is contained in:
Ricardo Wurmus 2021-12-09 09:16:53 +01:00
parent 0b8a75cc3a
commit 26e26bc819
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1 changed files with 41 additions and 38 deletions
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@ -5526,52 +5526,55 @@ (define-public minced
(license license:gpl3+)))
(define-public miso
(package
(name "miso")
(version "0.5.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "misopy" version))
(sha256
(base32
"1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
(modules '((guix build utils)))
(snippet '(begin
(substitute* "setup.py"
;; Use setuptools, or else the executables are not
;; installed.
(("distutils.core") "setuptools")
;; Use "gcc" instead of "cc" for compilation.
(("^defines")
"cc.set_executables(
(let ((commit "b71402188000465e3430736a11ea118fd5639a4a")
(revision "1"))
(package
(name "miso")
(version (git-version "0.5.4" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/yarden/MISO/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0x37ipwwvpxbkrg17gmq3hp92c9cphch8acd6cj7fqgnrjwd47g5"))
(modules '((guix build utils)))
(snippet
'(substitute* "setup.py"
;; Use "gcc" instead of "cc" for compilation.
(("^defines")
"cc.set_executables(
compiler='gcc',
compiler_so='gcc',
linker_exe='gcc',
linker_so='gcc -shared'); defines"))
#t))))
(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-mock" ,python2-mock) ; for tests
("python-pytz" ,python2-pytz))) ; for tests
(home-page "https://www.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
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 must not be newer than 1.2. See
;; https://github.com/yarden/MISO/issues/135
`(("samtools" ,samtools-1.2)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-scipy" ,python2-scipy)
("python-matplotlib" ,python2-matplotlib)))
(native-inputs
`(("python-mock" ,python2-mock) ; for tests
("python-pytz" ,python2-pytz))) ; for tests
(home-page "https://miso.readthedocs.io/en/fastmiso/")
(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)))
(license license:gpl2))))
(define-public muscle
(package