gnu: Add python-fanc.
* gnu/packages/bioinformatics.scm (python-fanc): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
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@ -10602,6 +10602,71 @@ traditional read alignments) and massively-parallel stochastic collapsed
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variational inference.")
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(license license:gpl3+)))
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(define-public python-fanc
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(package
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(name "python-fanc")
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(version "0.9.25")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/vaquerizaslab/fanc")
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;; There are no tags. This commit corresponds to
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;; version 0.9.25.
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(commit "e2205346c13ea5349681dff21adeb271d4ea5261")))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0rxq24p852iiayi0083fyigvc30as695rha71q6xd4s2ij1k9mqi"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:phases
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'(modify-phases %standard-phases
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(invoke "pytest" "-vv"
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"-k"
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;; XXX: These all fail because they fail to read
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;; the included test_{cooler,juicer}.hic files.
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(string-append "not test_edges_iter"
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" and not test_get_edges_uncorrected"
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" and not test_get_edges"))))))))
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(propagated-inputs
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(list python-biopython
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python-cooler
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python-deprecated
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python-future
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python-genomic-regions
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python-gridmap
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python-h5py
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python-intervaltree
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python-matplotlib
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python-msgpack
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python-msgpack-numpy
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python-numpy
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python-pandas
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python-pillow
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python-progressbar2
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python-pybedtools
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python-pybigwig
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python-pysam
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python-pytest
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python-pyyaml
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python-scikit-image
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python-scikit-learn
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python-scipy
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python-seaborn
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python-tables))
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(native-inputs
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(list python-cython))
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(home-page "https://github.com/vaquerizaslab/fanc")
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(synopsis "Framework for the analysis of C-data")
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(description
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"FAN-C provides a pipeline for analysing Hi-C data starting at
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mapped paired-end sequencing reads.")
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(license license:gpl3+)))
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(define-public python-genomic-regions
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(package
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(name "python-genomic-regions")
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