| Port details on branch 2022Q2 |
- py-biom-format Biological Observation Matrix (BIOM) Format Project
- 2.1.10_1 biology
 =0      2.1.10_1Version of this port present on the latest quarterly branch. - Maintainer: jrm@FreeBSD.org
- Port Added: 2016-05-09 16:37:53
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- Also Listed In: python
- License: BSD3CLAUSE
- WWW:
- https://biom-format.org/
- Description:
- The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-biom-format/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-biom-format
- pkg install py39-biom-format
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-biom-format listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-biom-format
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1610333968
SHA256 (biom-format-2.1.10.tar.gz) = f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488
SIZE (biom-format-2.1.10.tar.gz) = 11671341
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-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- cython-3.9 : lang/cython@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-click>0 : devel/py-click@py39
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-future>=0.16.0 : devel/py-future@py39
- py39-scipy>=1 : science/py-scipy@py39
- py39-pandas>=0.20.0 : math/py-pandas@py39
- py39-h5py>=2.2.0 : science/py-h5py@py39
- py39-six>=1.10.0 : devel/py-six@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/py-scikit-bio
Configuration Options:- No options to configure
- Options name:
- biology_py-biom-format
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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