diff options
author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-01-22 01:49:50 +0100 |
---|---|---|
committer | Ricardo Wurmus <rekado@elephly.net> | 2023-01-25 00:22:53 +0100 |
commit | 718223c58c20fa066527fb30da2b5dccca82913f (patch) | |
tree | 3c392b34c034b178db712b5bc3f27c9a593a784a /gnu/packages/bioinformatics.scm | |
parent | ed56d2a1c2b289c77174afac0c6b3b3bcae2e7ea (diff) | |
download | guix-718223c58c20fa066527fb30da2b5dccca82913f.tar.gz guix-718223c58c20fa066527fb30da2b5dccca82913f.zip |
gnu: Add python-phylophlan.
* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 37 |
1 files changed, 37 insertions, 0 deletions
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") |