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(license license:asl2.0))) +(define-public python-phylophlan + (package + (name "python-phylophlan") + (version "3.0.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "PhyloPhlAn" version)) + (sha256 + (base32 + "1r1bnnh4d38l410hfzf882y43ln8fd2lcsqbralqshxqw2hzc7x7")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f ;pypi no tests + #:phases + #~(modify-phases %standard-phases + ;;pypi does not provide the readme.md file + (add-before 'build 'loose-readme-file-requirement + (lambda _ + (substitute* "setup.py" + (("long_description") + "#long_description"))))))) + (propagated-inputs + (list python-biopython + python-dendropy + python-matplotlib + python-numpy + python-pandas + python-seaborn)) + (home-page "https://github.com/biobakery/phylophlan") + (synopsis + "Phylogenetic analysis of microbial isolates and genomes from metagenomes") + (description + "This package is an integrated pipeline for large-scale phylogenetic profiling +of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use +method for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. This software package can assign both genomes +and @acronym{MAGs, metagenome-assembled genomes} to @acronym{SGBs, species-level +genome bins}. PhyloPhlAn can reconstruct strain-level phylogenies using clade- +specific maximally informative phylogenetic markers, and can also scale to very +large phylogenies comprising >17,000 microbial species.") + (license license:expat))) + (define-public python-pybedtools (package (name "python-pybedtools")