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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-04-11 17:54:34 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-04-11 17:54:57 +0200 |
| commit | c2f6f4e50074ac12fa3bee51d793eeaadce99f55 (patch) | |
| tree | e933af8674bf44023fcb0cd0e775a5af6022be1f /gnu | |
| parent | 4fa16c9ae639c9891359527edc8c0b235e3987f2 (diff) | |
| download | patches-c2f6f4e50074ac12fa3bee51d793eeaadce99f55.tar patches-c2f6f4e50074ac12fa3bee51d793eeaadce99f55.tar.gz | |
gnu: Add python2-checkm-genome.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f1b670957..6ffd6acb60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14708,3 +14708,39 @@ downstream analysis.") `(("python-biopython" ,python2-biopython) ("taxtastic" ,taxtastic))) (synopsis "Pplacer Python scripts"))) + +(define-public python2-checkm-genome + (package + (name "python2-checkm-genome") + (version "1.0.13") + (source + (origin + (method url-fetch) + (uri (pypi-uri "checkm-genome" version)) + (sha256 + (base32 + "0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; some tests are interactive + (propagated-inputs + `(("python-dendropy" ,python2-dendropy) + ("python-matplotlib" ,python2-matplotlib) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-scipy" ,python2-scipy))) + (home-page "http://pypi.python.org/pypi/checkm/") + (synopsis "Assess the quality of putative genome bins") + (description + "CheckM provides a set of tools for assessing the quality of genomes +recovered from isolates, single cells, or metagenomes. It provides robust +estimates of genome completeness and contamination by using collocated sets of +genes that are ubiquitous and single-copy within a phylogenetic lineage. +Assessment of genome quality can also be examined using plots depicting key +genomic characteristics (e.g., GC, coding density) which highlight sequences +outside the expected distributions of a typical genome. CheckM also provides +tools for identifying genome bins that are likely candidates for merging based +on marker set compatibility, similarity in genomic characteristics, and +proximity within a reference genome.") + (license license:gpl3+))) |