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

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Message #11 received at 60997 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <60997 <at> debbugs.gnu.org>
Subject: [PATCH 4/4] gnu: Add python-metaphlan.
Date: Sun, 22 Jan 2023 01:49:51 +0100

* gnu/packages/bioinformatics.scm (python-metaphlan): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5c9c222d59..884e5aa1e5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11234,6 +11234,43 @@ (define-public python-biothings-client
 API services.")
     (license license:bsd-3)))
 
+(define-public python-metaphlan
+  (package
+    (name "python-metaphlan")
+    (version "4.0.4")
+    (source
+     (origin
+     (method url-fetch)
+              (uri (pypi-uri "MetaPhlAn" version))
+              (sha256
+               (base32
+                "1jw29m8p8bcwn4q5qvh8s96qlgqv1kaizbmm87jk55f34k1y3y8a"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:tests? #f)) ;pypi no tests
+    (propagated-inputs
+     (list python-biom-format
+           python-biopython
+           python-cmseq
+           python-dendropy
+           python-h5py
+           python-hclust2
+           python-numpy
+           python-pandas
+           python-phylophlan
+           python-pysam
+           python-requests
+           python-scipy))
+    (home-page "http://github.com/biobakery/MetaPhlAn/")
+    (synopsis "Metagenomic phylogenetic analysis")
+    (description
+     "MetaPhlAn is a computational tool for profiling the composition of microbial
+communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing
+data (i.e.  not 16S) with species-level.  With the newly added StrainPhlAn module,
+it is now possible to perform accurate strain-level microbial profiling.")
+    (license license:expat)))
+
 (define-public python-multivelo
   (package
     (name "python-multivelo")
-- 
2.39.1

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