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authorRicardo Wurmus <rekado@elephly.net>2023-05-03 11:58:51 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-05-03 11:59:54 +0200
commit83a6ca3c60155479525bbf01e7b9509a994c7d03 (patch)
tree63958b0d95116508723cb09b91863712c585fb65
parentbfe513eeb39a3325d1d8a6e23121f7ab4165a874 (diff)
downloadguix-83a6ca3c60155479525bbf01e7b9509a994c7d03.tar.gz
guix-83a6ca3c60155479525bbf01e7b9509a994c7d03.zip
gnu: Add fanc.
* gnu/packages/bioinformatics.scm (fanc): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm58
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 83ee4ac1df..8d739d4b52 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4655,6 +4655,64 @@ variety of diversity measures including those that make use of phylogenetic
similarity of community members.")
(license license:gpl3+)))
+(define-public fanc
+ (let ((commit "354401e52ba2320e6b1ba0d3b5aab3541d31c9f3")
+ (revision "1"))
+ (package
+ (name "fanc")
+ (version (git-version "0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vaquerizaslab/fanc.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0vp2cak5snla4j2q23d3ixx016bwzvxfiv4z6yp7anl0xaksd5bl"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ '(list "-m" "not longrunning"
+ ;; XXX: some of the tests here just take forever
+ "--ignore=fanc/test/test_matrix.py")))
+ (propagated-inputs
+ (list python-biopython
+ python-cooler
+ python-deprecated
+ python-future
+ python-genomic-regions
+ python-gridmap
+ python-h5py
+ python-imageio
+ python-intervaltree
+ python-matplotlib
+ python-msgpack
+ python-msgpack-numpy
+ python-numpy
+ python-pandas
+ python-pillow
+ python-progressbar2
+ python-pybedtools
+ python-pybigwig
+ python-pysam
+ python-pywavelets
+ python-pyyaml
+ python-scikit-image
+ python-scikit-learn
+ python-scipy
+ python-seaborn
+ python-tables
+ python-tifffile))
+ (native-inputs
+ (list python-cython python-pytest))
+ (home-page "https://github.com/vaquerizaslab/fanc")
+ (synopsis "Framework for the analysis of C-like data")
+ (description "FAN-C provides a pipeline for analysing Hi-C data starting
+at mapped paired-end sequencing reads.")
+ (license license:gpl3+))))
+
(define-public fasttree
(package
(name "fasttree")