gnu: Add python-hicexplorer.
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
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@ -13615,3 +13615,56 @@ fasta subsequences.")
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storage format, called @code{cool}, used to store genomic interaction data,
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storage format, called @code{cool}, used to store genomic interaction data,
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such as Hi-C contact matrices.")
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such as Hi-C contact matrices.")
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(license license:bsd-3)))
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(license license:bsd-3)))
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(define-public python-hicexplorer
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(package
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(name "python-hicexplorer")
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(version "2.1.4")
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(source
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(origin
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;; The latest version is not available on Pypi.
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/deeptools/HiCExplorer.git")
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(commit version)))
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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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"0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'loosen-up-requirements
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(lambda _
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(substitute* "setup.py"
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(("==") ">="))
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#t)))))
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(propagated-inputs
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`(("python-biopython" ,python-biopython)
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("python-configparser" ,python-configparser)
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("python-cooler" ,python-cooler)
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("python-future" ,python-future)
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("python-intervaltree" ,python-intervaltree)
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("python-jinja2" ,python-jinja2)
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("python-matplotlib" ,python-matplotlib)
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("python-numpy" ,python-numpy)
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("python-pandas" ,python-pandas)
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("python-pybigwig" ,python-pybigwig)
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("python-pysam" ,python-pysam)
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("python-scipy" ,python-scipy)
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("python-six" ,python-six)
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("python-tables" ,python-tables)
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("python-unidecode" ,python-unidecode)))
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(home-page "http://hicexplorer.readthedocs.io")
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(synopsis "Process, analyze and visualize Hi-C data")
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(description
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"HiCExplorer is a powerful and easy to use set of tools to process,
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normalize and visualize Hi-C data. HiCExplorer facilitates the creation of
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contact matrices, correction of contacts, TAD detection, A/B compartments,
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merging, reordering or chromosomes, conversion from different formats
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including cooler and detection of long-range contacts. Moreover, it allows
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the visualization of multiple contact matrices along with other types of data
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like genes, compartments, ChIP-seq coverage tracks (and in general any type of
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genomic scores), long range contacts and the visualization of viewpoints.")
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(license license:gpl3)))
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