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06/09: gnu: miso: Update to 0.5.4-1.b714021.
From: |
guix-commits |
Subject: |
06/09: gnu: miso: Update to 0.5.4-1.b714021. |
Date: |
Thu, 9 Dec 2021 05:20:14 -0500 (EST) |
rekado pushed a commit to branch core-updates-frozen
in repository guix.
commit 26e26bc8191604f0125ccbdc231498545f93dc5c
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Dec 9 09:16:53 2021 +0100
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.
---
gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++--------------------
1 file changed, 41 insertions(+), 38 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 13901bc..70eb130 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5526,52 +5526,55 @@ assembled metagenomic sequence.")
(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
- branch core-updates-frozen updated (95a4965 -> ab445eb), guix-commits, 2021/12/09
- 08/09: gnu: seek: Update to 1-1.196ed4c., guix-commits, 2021/12/09
- 04/09: gnu: Add htslib-for-samtools-1.2., guix-commits, 2021/12/09
- 02/09: gnu: python2-matplotlib: Fix mpl_toolkits module., guix-commits, 2021/12/09
- 03/09: gnu: python2-scipy: Override native inputs., guix-commits, 2021/12/09
- 09/09: gnu: python2-scikit-learn: Disable one more test., guix-commits, 2021/12/09
- 01/09: gnu: Add gfortran-7., guix-commits, 2021/12/09
- 05/09: gnu: Add samtools-1.2., guix-commits, 2021/12/09
- 06/09: gnu: miso: Update to 0.5.4-1.b714021.,
guix-commits <=
- 07/09: gnu: libsvm: Install header and library., guix-commits, 2021/12/09