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-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d66d9ef40e..65da049c79 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13578,3 +13578,40 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
"This package provides procedures for efficient pythonic random access to
fasta subsequences.")
(license license:bsd-3)))
+
+(define-public python-cooler
+ (package
+ (name "python-cooler")
+ (version "0.7.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cooler" version))
+ (sha256
+ (base32
+ "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-biopython" ,python-biopython)
+ ("python-click" ,python-click)
+ ("python-cytoolz" ,python-cytoolz)
+ ("python-dask" ,python-dask)
+ ("python-h5py" ,python-h5py)
+ ("python-multiprocess" ,python-multiprocess)
+ ("python-pandas" ,python-pandas)
+ ("python-pyfaidx" ,python-pyfaidx)
+ ("python-pypairix" ,python-pypairix)
+ ("python-pysam" ,python-pysam)
+ ("python-scipy" ,python-scipy)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-nose" ,python-nose)
+ ("python-numpydoc" ,python-numpydoc)
+ ("python-sphinx" ,python-sphinx)))
+ (home-page "https://github.com/mirnylab/cooler")
+ (synopsis "Sparse binary format for genomic interaction matrices")
+ (description
+ "Cooler is a support library for a sparse, compressed, binary persistent
+storage format, called @code{cool}, used to store genomic interaction data,
+such as Hi-C contact matrices.")
+ (license license:bsd-3)))