| Port details on branch 2022Q2 |
- checkm Quality assessment tool for the microbial genomes
- 1.2.2 biology
 =0      1.2.0_1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-07 00:26:14
- Last Update: 2024-04-23 08:40:35
- Commit Hash: 7336b01
- Also Listed In: python
- License: GPLv3
- WWW:
- https://ecogenomics.github.io/CheckM/
- 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 tree.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/checkm/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/checkm
- pkg install CheckM
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: CheckM
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1713784123
SHA256 (Ecogenomics-CheckM-v1.2.2_GH0.tar.gz) = a748b94e93f8d5fecfd0d5b3f17fcb119b25d4b45217e047b2fd742b21e74c0e
SIZE (Ecogenomics-CheckM-v1.2.2_GH0.tar.gz) = 1017249
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
- py39-DendroPy>0 : science/py-DendroPy@py39
- py39-matplotlib>0 : math/py-matplotlib@py39
- py39-pysam>0 : biology/py-pysam@py39
- py39-scipy>0 : science/py-scipy@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_checkm
- USES:
- dos2unix python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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