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authorRicardo Wurmus <rekado@elephly.net>2021-08-31 23:10:42 +0200
committerRicardo Wurmus <rekado@elephly.net>2021-08-31 23:11:06 +0200
commit4abf2268338f34fc85a24e14a3bbcc6803fa0e82 (patch)
tree5e8bb2b9e50830b083061d5176995f6e314b7b7f
parenta1ee2121843d2b7eea2dc932f16d543ae7ff7007 (diff)
downloadguix-4abf2268338f34fc85a24e14a3bbcc6803fa0e82.tar
guix-4abf2268338f34fc85a24e14a3bbcc6803fa0e82.tar.gz
gnu: Add scregseg.
* gnu/packages/bioinformatics.scm (scregseg): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm50
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c199883829..aef9625534 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14949,6 +14949,56 @@ line, interactively explore genomic data within Jupyter environment or web
browser.")
(license license:gpl3+)))
+(define-public scregseg
+ (package
+ (name "scregseg")
+ (version "0.1.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BIMSBbioinfo/scregseg")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #false ; tests require network access
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-fail-to-find-sklearn
+ (lambda _
+ ;; XXX: I have no idea why it cannot seem to find sklearn.
+ (substitute* "setup.py"
+ (("'sklearn',") "")))))))
+ (native-inputs
+ `(("python-cython" ,python-cython)))
+ (propagated-inputs
+ `(("python-scikit-learn" ,python-scikit-learn)
+ ("python-scipy" ,python-scipy)
+ ("python-numpy" ,python-numpy)
+ ("python-hmmlearn" ,python-hmmlearn)
+ ("python-pandas" ,python-pandas)
+ ("python-numba" ,python-numba)
+ ("python-anndata" ,python-anndata)
+ ("python-scanpy" ,python-scanpy)
+ ("python-pybedtools" ,python-pybedtools)
+ ("python-pysam" ,python-pysam)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-seaborn" ,python-seaborn)
+ ("python-coolbox" ,python-coolbox)))
+ (home-page "https://github.com/BIMSBbioinfo/scregseg")
+ (synopsis "Single-cell regulatory landscape segmentation")
+ (description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a
+tool that facilitates the analysis of single cell ATAC-seq data by an
+HMM-based segmentation algorithm. Scregseg uses an HMM with
+Dirichlet-Multinomial emission probabilities to segment the genome either
+according to distinct relative cross-cell accessibility profiles or (after
+collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct
+cross-cluster accessibility profiles.")
+ (license license:gpl3+)))
+
(define-public r-ascat
(package
(name "r-ascat")