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06/06: gnu: Add python-phylophlan.
From: |
guix-commits |
Subject: |
06/06: gnu: Add python-phylophlan. |
Date: |
Tue, 24 Jan 2023 18:23:51 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 718223c58c20fa066527fb30da2b5dccca82913f
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Sun Jan 22 01:49:50 2023 +0100
gnu: Add python-phylophlan.
* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 063fe7f094..6cb5ea99eb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1103,6 +1103,43 @@ protocol. It provides a simple and reliable way to
retrieve genomic data from
servers supporting the protocol.")
(license license:asl2.0)))
+(define-public python-phylophlan
+ (package
+ (name "python-phylophlan")
+ (version "3.0.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biobakery/phylophlan")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wz70xzxqx2sf5flmf45m15jq027dqijfaj1r51pl50w5x6dkawx"))))
+ (build-system pyproject-build-system)
+ (arguments (list #:tests? #f)) ;there are no tests
+ (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")
- branch master updated (f9c151b936 -> 718223c58c), guix-commits, 2023/01/24
- 04/06: gnu: Add python-cmseq., guix-commits, 2023/01/24
- 03/06: gnu: Add python-bcbio-gff/biopython-1.73., guix-commits, 2023/01/24
- 05/06: gnu: Add python-hclust2., guix-commits, 2023/01/24
- 02/06: gnu: Add emacs-malyon., guix-commits, 2023/01/24
- 01/06: gnu: Add synthpod., guix-commits, 2023/01/24
- 06/06: gnu: Add python-phylophlan.,
guix-commits <=