svn commit: r486814 - in head/biology: . checkm
Yuri Victorovich
yuri at FreeBSD.org
Fri Dec 7 00:26:06 UTC 2018
Author: yuri
Date: Fri Dec 7 00:26:04 2018
New Revision: 486814
URL: https://svnweb.freebsd.org/changeset/ports/486814
Log:
New port: math/checkm: Quality assessment tool for the microbial genomes
Added:
head/biology/checkm/
head/biology/checkm/Makefile (contents, props changed)
head/biology/checkm/distinfo (contents, props changed)
head/biology/checkm/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Fri Dec 7 00:12:55 2018 (r486813)
+++ head/biology/Makefile Fri Dec 7 00:26:04 2018 (r486814)
@@ -16,6 +16,7 @@
SUBDIR += canu
SUBDIR += cd-hit
SUBDIR += cdbfasta
+ SUBDIR += checkm
SUBDIR += chemeq
SUBDIR += clustal-omega
SUBDIR += clustalw
Added: head/biology/checkm/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/checkm/Makefile Fri Dec 7 00:26:04 2018 (r486814)
@@ -0,0 +1,27 @@
+# $FreeBSD$
+
+PORTNAME= CheckM
+DISTVERSIONPREFIX= v
+DISTVERSION= 1.0.12
+CATEGORIES= biology python
+
+MAINTAINER= yuri at 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>
Added: head/biology/checkm/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/checkm/distinfo Fri Dec 7 00:26:04 2018 (r486814)
@@ -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
Added: head/biology/checkm/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/checkm/pkg-descr Fri Dec 7 00:26:04 2018 (r486814)
@@ -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/
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