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

* 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.
master
Ricardo Wurmus 2021-12-09 09:16:53 +01:00
parent 0b8a75cc3a
commit 26e26bc819
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GPG Key ID: 197A5888235FACAC
1 changed files with 41 additions and 38 deletions
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@ -5526,35 +5526,38 @@ assembled metagenomic sequence.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public miso (define-public miso
(let ((commit "b71402188000465e3430736a11ea118fd5639a4a")
(revision "1"))
(package (package
(name "miso") (name "miso")
(version "0.5.4") (version (git-version "0.5.4" revision commit))
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (pypi-uri "misopy" version)) (uri (git-reference
(url "https://github.com/yarden/MISO/")
(commit commit)))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) "0x37ipwwvpxbkrg17gmq3hp92c9cphch8acd6cj7fqgnrjwd47g5"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet '(begin (snippet
(substitute* "setup.py" '(substitute* "setup.py"
;; Use setuptools, or else the executables are not
;; installed.
(("distutils.core") "setuptools")
;; Use "gcc" instead of "cc" for compilation. ;; Use "gcc" instead of "cc" for compilation.
(("^defines") (("^defines")
"cc.set_executables( "cc.set_executables(
compiler='gcc', compiler='gcc',
compiler_so='gcc', compiler_so='gcc',
linker_exe='gcc', linker_exe='gcc',
linker_so='gcc -shared'); defines")) linker_so='gcc -shared'); defines")))))
#t))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2 ; only Python 2 is supported `(#:python ,python-2 ; only Python 2 is supported
#:tests? #f)) ; no "test" target #:tests? #f)) ; no "test" target
(inputs (inputs
`(("samtools" ,samtools) ;; 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-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam) ("python-pysam" ,python2-pysam)
("python-scipy" ,python2-scipy) ("python-scipy" ,python2-scipy)
@ -5562,7 +5565,7 @@ linker_so='gcc -shared'); defines"))
(native-inputs (native-inputs
`(("python-mock" ,python2-mock) ; for tests `(("python-mock" ,python2-mock) ; for tests
("python-pytz" ,python2-pytz))) ; for tests ("python-pytz" ,python2-pytz))) ; for tests
(home-page "https://www.genes.mit.edu/burgelab/miso/index.html") (home-page "https://miso.readthedocs.io/en/fastmiso/")
(synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
(description (description
"MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
@ -5571,7 +5574,7 @@ identifies differentially regulated isoforms or exons across samples. By
modeling the generative process by which reads are produced from isoforms in modeling the generative process by which reads are produced from isoforms in
RNA-Seq, the MISO model uses Bayesian inference to compute the probability RNA-Seq, the MISO model uses Bayesian inference to compute the probability
that a read originated from a particular isoform.") that a read originated from a particular isoform.")
(license license:gpl2))) (license license:gpl2))))
(define-public muscle (define-public muscle
(package (package