From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <60997@debbugs.gnu.org>
Cc: rekado@elephly.net
Subject: [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan.
Date: Sun, 22 Jan 2023 01:49:50 +0100 [thread overview]
Message-ID: <20230122004951.119277-3-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de>
* 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
next prev parent reply other threads:[~2023-01-22 0:51 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-01-22 0:44 [bug#60997] [patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and python-metaphlan MadalinIonel.Patrascu
2023-01-22 0:49 ` [bug#60997] [PATCH 1/4] gnu: Add python-cmseq Mădălin Ionel Patrașcu
2023-01-22 0:49 ` [bug#60997] [PATCH 2/4] gnu: Add python-hclust2 Mădălin Ionel Patrașcu
2023-01-22 0:49 ` Mădălin Ionel Patrașcu [this message]
2023-01-24 9:10 ` [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan Ricardo Wurmus
2023-01-22 0:49 ` [bug#60997] [PATCH 4/4] gnu: Add python-metaphlan Mădălin Ionel Patrașcu
2023-01-24 9:11 ` Ricardo Wurmus
2023-01-24 8:36 ` [bug#60997] [PATCH 1/4] gnu: Add python-cmseq Ricardo Wurmus
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