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Port details
pycogent Toolkit for statistical analysis of biological sequences
1.5.3_3 biology on this many watch lists=0 search for ports that depend on this port
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Jun 2009 12:47:26
Also Listed In: python
License: GPLv2


PyCogent is a software library for genomic biology. It is a fully integrated
and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.

WWW: http://pycogent.sourceforge.net/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

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

Required To Build:
  1. math/py-numpy
  2. lang/cython
  3. textproc/py-sphinx
  4. databases/py-sqlalchemy06
  5. devel/py-setuptools27
  6. lang/python27
Required To Run:
  1. math/py-numpy
  2. lang/cython
  3. textproc/py-sphinx
  4. databases/py-sqlalchemy06
  5. devel/py-setuptools27
  6. lang/python27
There are no ports dependent upon this port

To install the port: cd /usr/ports/biology/pycogent/ && make install clean
To add the package: pkg install biology/pycogent


Configuration Options
     No options to configure

Master Sites:
  1. http://aarnet.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  2. http://distcache.FreeBSD.org/ports-distfiles/
  3. http://downloads.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  4. http://freefr.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  5. http://garr.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  6. http://heanet.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  7. http://hivelocity.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  8. http://ignum.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  9. http://internode.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  10. http://iweb.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  11. http://jaist.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  12. http://kaz.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  13. http://kent.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  14. http://master.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  15. http://nchc.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  16. http://ncu.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  17. http://netcologne.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  18. http://sunet.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  19. http://superb-dca3.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  20. http://switch.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  21. http://tenet.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  22. http://ufpr.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/
  23. http://waix.dl.sourceforge.net/project/pycogent/PyCogent/1.5.3/

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Oct 2014 07:38:12
Original commit files touched by this commit  1.5.3_3
Revision:371171
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
10 Sep 2014 20:50:37
Original commit files touched by this commit  1.5.3_3
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
02 May 2014 14:00:13
Original commit files touched by this commit  1.5.3_2
Revision:352814
wen search for other commits by this committer
- Stage support [1]
- Pet portlint [1]
- Add LICENSE
- Convert to PYDISTUTILS_AUTOPLIST

PR:		188819 [1]
Submitted by:	Bartek Rutkowski <ports@robakdesign.com> [1]
10 Mar 2014 20:55:22
Original commit files touched by this commit  1.5.3_2
Revision:347809
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
26 Oct 2013 00:52:36
Original commit files touched by this commit  1.5.3_1
Revision:331644
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.5.3
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
08 Oct 2012 03:17:03
Original commit files touched by this commit  1.5.3
Revision:305516
wen search for other commits by this committer
- Update to 1.5.3
- Trim Makefile headers
10 Jun 2012 18:42:48
Original commit files touched by this commit  1.5.1
swills search for other commits by this committer
- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or
  RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned
  about for a while.

PR:             ports/168208
Approved by:    portmgr (miwi)
11 Aug 2011 11:37:18
Original commit files touched by this commit  1.5.1
wen search for other commits by this committer
- Update to 1.5.1
25 Jun 2011 07:21:20
Original commit files touched by this commit  1.5_1
nivit search for other commits by this committer
- Fix *_DEPENDS after the repocopy of databases/py-sqlalchemy
  (This port doesn't yet support SQLAlchemy 0.7.X)
- Bump PORTREVISION
10 Nov 2010 08:52:26
Original commit files touched by this commit  1.5
wen search for other commits by this committer
- Update to 1.5.0
01 Jun 2010 06:57:30
Original commit files touched by this commit  1.4.1
wen search for other commits by this committer
- Update to 1.4.1
17 Dec 2009 06:51:53
Original commit files touched by this commit  1.4
wen search for other commits by this committer
- Update to 1.4
- Update my mail address to FreeBSD
22 Aug 2009 00:15:15
Original commit files touched by this commit  1.3.1
amdmi3 search for other commits by this committer
- Switch SourceForge ports to the new File Release System: categories starting
with B,C
22 Jun 2009 12:46:56
Original commit files touched by this commit  1.3.1
miwi search for other commits by this committer
PyCogent is a software library for genomic biology. It is a fully integrated
and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.

WWW:    http://pycogent.sourceforge.net/

PR:             ports/135863
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 15

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