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New port: math/checkm: Quality assessment tool for the microbial genomes

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This commit is contained in:
Yuri Victorovich 2018-12-07 00:26:04 +00:00
parent 74fe36ceb2
commit ad4ef5b010
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=486814
4 changed files with 43 additions and 0 deletions
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1
biology/Makefile
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@ -16,6 +16,7 @@
SUBDIR += canu
SUBDIR += cd-hit
SUBDIR += cdbfasta
SUBDIR += checkm
SUBDIR += chemeq
SUBDIR += clustal-omega
SUBDIR += clustalw

27
biology/checkm/Makefile Normal file
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@ -0,0 +1,27 @@
# $FreeBSD$
PORTNAME= CheckM
DISTVERSIONPREFIX= v
DISTVERSION= 1.0.12
CATEGORIES= biology python
MAINTAINER= yuri@FreeBSD.org
COMMENT= Quality assessment tool for the microbial genomes
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/LICENSE
RUN_DEPENDS= ${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}DendroPy>=4.0.0:science/py-DendroPy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}matplotlib>=1.3.1:math/py-matplotlib@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pysam>=0.8.3:biology/py-pysam@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>=0.9.0:science/py-scipy@${PY_FLAVOR}
USES= python
USE_GITHUB= yes
GH_ACCOUNT= Ecogenomics
USE_PYTHON= distutils noflavors autoplist
NO_ARCH= yes
.include <bsd.port.mk>

3
biology/checkm/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1544141583
SHA256 (Ecogenomics-CheckM-v1.0.12_GH0.tar.gz) = 4aca26d0ae903ed7567cfc6ec53dc1d2ea909d58a0c4c6e2318a1885abbcfd91
SIZE (Ecogenomics-CheckM-v1.0.12_GH0.tar.gz) = 211396

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biology/checkm/pkg-descr Normal file
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@ -0,0 +1,12 @@
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 tree.
WWW: https://ecogenomics.github.io/CheckM/