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authorRicardo Wurmus <rekado@elephly.net>2019-04-11 17:54:34 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-04-11 17:54:57 +0200
commitc2f6f4e50074ac12fa3bee51d793eeaadce99f55 (patch)
treee933af8674bf44023fcb0cd0e775a5af6022be1f /gnu/packages
parent4fa16c9ae639c9891359527edc8c0b235e3987f2 (diff)
gnu: Add python2-checkm-genome.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm36
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+)))