GNU bug report logs - #60997
[patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and python-metaphlan.

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <60997 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net
Subject: [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan.
Date: Sun, 22 Jan 2023 01:49:50 +0100

* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.
---
 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf01c9c7e4..5c9c222d59 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")
-- 
2.39.1

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