@@ -1089,6 +1089,49 @@ (define-public python-htsget
servers supporting the protocol.")
(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")