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Port details
py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.6 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 09 May 2016 16:37:53
Also Listed In: python
License: BSD3CLAUSE
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.

WWW: http://biom-format.org/
SVNWeb : Homepage : PortsMon

To install the port: cd /usr/ports/biology/py-biom-format/ && make install clean
To add the package: pkg install py27-biom-format

PKGNAME: py27-biom-format

ONLY_FOR_ARCHS: nil

NOT_FOR_ARCHS: nil

distinfo:

TIMESTAMP = 1493465225
SHA256 (biocore-biom-format-2.1.6_GH0.tar.gz) = f2daddb634c540e10d04e4f71174da98f57d7f95472f02c358df4ca82e3f9921
SIZE (biocore-biom-format-2.1.6_GH0.tar.gz) = 11997159


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. numeric.py : math/py-numpy
  2. py27-setuptools>0 : devel/py27-setuptools
  3. python2.7 : lang/python27
Runtime dependencies:
  1. numeric.py : math/py-numpy
  2. py27-h5py>=2.6.0 : science/py-h5py
  3. py27-click>=6.6 : devel/py-click
  4. py27-future>=0.15.2 : devel/py-future
  5. py27-scipy>=0.16.1 : science/py-scipy
  6. py27-setuptools>0 : devel/py27-setuptools
  7. python2.7 : lang/python27
  8. py27-pyqi>=0.2.0 : devel/py-pyqi
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
python

Master Sites:
  1. https://codeload.github.com/biocore/biom-format/tar.gz/2.1.6?dummy=/

Number of commits found: 5

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
29 Apr 2017 13:59:15
Original commit files touched by this commit  2.1.6
Revision:439751
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.6

Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.6

Approved by:	swills (mentor, implicit)
23 Sep 2016 21:42:02
Original commit files touched by this commit  2.1.5_1
Revision:422697
jrm search for other commits by this committer
Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995
11 Jun 2016 09:25:04
Original commit files touched by this commit  2.1.5_1
Revision:416710
olivierd search for other commits by this committer
- Fix run-time dependency issues
- Bump PORTREVISION

PR:		209767
Submitted by:	Joseph Mingrone (maintainer)
09 May 2016 16:42:17
Original commit files touched by this commit  2.1.5
Revision:414866
olivierd search for other commits by this committer
Add final slash in WWW entry
09 May 2016 16:37:44
Original commit files touched by this commit  2.1.5
Revision:414865
olivierd search for other commits by this committer
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.

WWW: http://biom-format.org/

PR:		209193
Submitted by:	Joseph Mingrone

Number of commits found: 5

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