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

git-svn-id: svn+ssh://svn.freebsd.org/ports/head@486814 35697150-7ecd-e111-bb59-0022644237b5

biology/Makefile

@@ -16,6 +16,7 @@
     SUBDIR += canu
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
+    SUBDIR += checkm
     SUBDIR += chemeq
     SUBDIR += clustal-omega
     SUBDIR += clustalw

biology/checkm/Makefile

@@ -0,0 +1,27 @@
+# $FreeBSD$
+
+PORTNAME=	CheckM
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.0.12
+CATEGORIES=	biology python
+
+MAINTAINER=	[email protected]
+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>

biology/checkm/distinfo

@@ -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

biology/checkm/pkg-descr

@@ -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/