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Port details
py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.6_1 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
There is no configure plist information for this port

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

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. py27-numpy>0 : math/py-numpy@py27
  2. py27-setuptools>0 : devel/py-setuptools@py27
  3. python2.7 : lang/python27
Runtime dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. py27-click>=6.6 : devel/py-click@py27
  3. py27-future>=0.15.2 : devel/py-future@py27
  4. py27-pandas>0 : math/py-pandas@py27
  5. py27-h5py>=2.6.0 : science/py-h5py@py27
  6. py27-scipy>=0.16.1 : science/py-scipy@py27
  7. py27-setuptools>0 : devel/py-setuptools@py27
  8. python2.7 : lang/python27
  9. py27-pyqi>=0.2.0 : devel/py-pyqi@py27
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=/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Dec 2017 03:33:04
Original commit files touched by this commit  2.1.6_1
Revision:455879
jrm search for other commits by this committer
biology/py-biom-format: Add required dependency on math/py-pandas and do
not install tests.
30 Nov 2017 15:50:34
Original commit files touched by this commit  2.1.6
Revision:455210  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
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: 7

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