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Port details
py-biopython Collection of Python modules for bioinformatics
1.60_4 biology on this many watch lists=3 search for ports that depend on this port
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 31 Jul 2000 09:12:24
Also Listed In: python
License: not specified in port


The Biopython Project is an international association of developers who are
providing freely available Python tools for use in areas of computational
molecular biology such as bioinformatics and genomics.

Biopython is a collection of Python packages and modules created by the
Biopython Project, intended to provide the basis for building bioinformatics
applications in the Python language.

Note that the current release is alpha quality, and not yet deemed to be
stable.

This port includes optional support for Biopython-CORBA, a CORBA interface
built to the BioCorba standard (http://biocorba.org/).

WWW: http://biopython.org/
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. devel/py-setuptools27
  3. lang/python27
  4. lang/python2
Required To Run:
  1. math/py-numpy
  2. print/py-reportlab1
  3. devel/py-setuptools27
  4. lang/python27
  5. lang/python2
There are no ports dependent upon this port

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


Configuration Options
     No options to configure

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/
  2. http://www.biopython.org/DIST/

Number of commits found: 49

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  1.60_4
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  1.60_4
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)
27 Apr 2014 01:59:47
Original commit files touched by this commit  1.60_3
Revision:352389
swills search for other commits by this committer
- Stage
- Drop easy_install
- Use auto pkg-plist
- Delete pkg-plist

PR:		ports/188818
Submitted by:	Bartek Rutkowski <ports@robakdesign.com>
Approved by:	portmgr@ (blanket)
10 Mar 2014 20:55:22
Original commit files touched by this commit  1.60_3
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)
25 Feb 2014 12:44:10
Original commit files touched by this commit  1.60_2
Revision:345987
tota search for other commits by this committer
- Repocopy print/py-reportlab to print/py-reportlab1
  to preserve version 1.x and to update to 3.0

  print/py-reportlab:
    - Update print/py-reportlab to 3.0 based on print/py-reportlab2
    - Support STAGEDIR
    - Use PYDISTUTILS_AUTOPLIST
      * Remove pkg-plist, accordingly
    - Set CONFLICTS
    - Add PORTSCOUT
    - Replace tab with a single space after WWW: in pkg-descr

  print/py-reportlab1:
    - Support STAGEDIR
    - Add PKGNAMESUFFIX not to duplicate ports with the same name
(Only the first 15 lines of the commit message are shown above View all of this commit message)
13 Jan 2014 21:00:04
Original commit files touched by this commit  1.60_1
Revision:339634
rene search for other commits by this committer
Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by:	python (mva, rm)
Approved by:	portmgr-lurkers (mat)
26 Oct 2013 00:52:36
Original commit files touched by this commit  1.60_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  1.60
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)
25 Sep 2012 08:06:43
Original commit files touched by this commit  1.60
Revision:304822
rm search for other commits by this committer
- update to 1.60

while here:
- convert Makefile header into two-line format
- update COMMENT (indefinite article removed)
- change USE_PYTHON to just -2.7
- remove py-reportlab from BUILD_DEPENDS and kick PYTHON_SITELIBDIR from there
- tab -> space change in pkg-descr:WWW

PR:		171115
Submitted by:	wen
Approved by:	Mauricio Herrera Cuadra <mauricio at arareko dot net> (maintainer)
06 Mar 2012 06:40:50
Original commit files touched by this commit  1.59
wen search for other commits by this committer
- Update to 1.59

PR:             ports/165582
Submitted by:   wen@ (myself)
Approved by:    Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer, via
email)
22 Oct 2011 23:50:23
Original commit files touched by this commit  1.57
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
24 May 2011 09:06:29
Original commit files touched by this commit  1.57
wen search for other commits by this committer
- Update to 1.57

PR:             ports/156329
Submitted by:   Wen Heping (myself)
Approved by:    maintainer
24 Feb 2011 23:25:54
Original commit files touched by this commit  1.54_1
miwi search for other commits by this committer
- Move over to python2.5 or higher
- While here kick md5
02 Jul 2010 02:57:19
Original commit files touched by this commit  1.54
wen search for other commits by this committer
- Update to 1.54

PR:             ports/148274
Submitted by:   Ju Pengfei <jupengfei@gmail.com>
Approved by:    maintainer
Feature safe:   yes
06 Jan 2010 00:29:25
Original commit files touched by this commit  1.53
wen search for other commits by this committer
- Update to 1.53

PR:             ports/142221
Submitted by:   Wen Heping (myself)
Approved by:    maintainer
04 Sep 2009 20:41:25
Original commit files touched by this commit  1.51
miwi search for other commits by this committer
- Update to 138038

PR:             138038
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer
11 Oct 2008 15:26:33
Original commit files touched by this commit  1.48
miwi search for other commits by this committer
- Update to 1.48

PR:             127776
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    maintainer
11 Aug 2008 22:06:31
Original commit files touched by this commit  1.47
miwi search for other commits by this committer
- Update to 1.47

PR:             125912
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    maintainer timeout
04 Jul 2008 02:53:15
Original commit files touched by this commit  1.45
beech search for other commits by this committer
- Update to 1.45

PR:             ports/125134
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
31 May 2007 03:49:14
Original commit files touched by this commit  1.43
miwi search for other commits by this committer
- Fix typos.

Reported by:    stas@
30 May 2007 06:57:20
Original commit files touched by this commit  1.43
miwi search for other commits by this committer
- Update to 1.43

PR:             111817
Submitted by:   "P.BandieraPaiva" <paiva@unifesp.br>
Approved by:    maintainer
31 Oct 2006 13:25:21
Original commit files touched by this commit  1.42
miwi search for other commits by this committer
- Update to 1.42

PR:             ports/104635
Submitted by:   Thomas Abthorpe <thomas@goodking.ca>
Approved by:    maintainer
11 Nov 2005 01:15:35
Original commit files touched by this commit  1.41
mnag search for other commits by this committer
Update to 1.41
Take MAINTAINER
Add SHA256

PR:             88792
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
02 Dec 2004 05:51:25
Original commit files touched by this commit  1.30
perky search for other commits by this committer
Fix build on Python 2.4

Spotted by:     kris
20 Nov 2004 08:09:49
Original commit files touched by this commit  1.30
linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
06 Nov 2004 23:12:14
Original commit files touched by this commit  1.30
pav search for other commits by this committer
- Fix build on amd64 (crude hack to pass -fPIC to c++ compiles)

Reported by:    pointyhat via kris
Tested on:      arved's box
27 Oct 2004 20:39:17
Original commit files touched by this commit  1.30
pav search for other commits by this committer
- Update to 1.30

PR:             ports/71400
Submitted by:   Stefan Walter <sw@gegenunendlich.de>
Approved by:    maintainer timeout (2 months)
02 Jul 2004 08:20:02
Original commit files touched by this commit  1.23
kris search for other commits by this committer
BROKEN: Does not build
31 Mar 2004 03:12:58
Original commit files touched by this commit  1.23
trevor search for other commits by this committer
SIZEify (maintainer timeout)
09 Feb 2004 21:40:48
Original commit files touched by this commit  1.23
des search for other commits by this committer
Upgrade to 1.23.

Approved by:    maintainer timeout
20 Nov 2003 15:06:15
Original commit files touched by this commit  1.00.a4
trevor search for other commits by this committer
Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:   Oliver Eikemeier
20 Nov 2003 13:51:47
Original commit files touched by this commit  1.00.a4
trevor search for other commits by this committer
Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.
13 Nov 2003 14:45:08
Original commit files touched by this commit  1.00.a4
trevor search for other commits by this committer
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
22 Oct 2003 09:29:55
Original commit files touched by this commit  1.00.a4
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
01 Aug 2003 22:04:57
Original commit files touched by this commit  1.00.a4
perky search for other commits by this committer
Fix python version detection routines to cope with python 2.3's
boolean representation.
07 Mar 2003 05:56:43
Original commit files touched by this commit  1.00.a4
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
15 Jul 2002 11:37:35
Original commit files touched by this commit  1.00.a4
tg search for other commits by this committer
Use $PYNUMERIC in the dependencies.
22 Jan 2002 10:54:02
files touched by this commit
wjv search for other commits by this committer
- Update to version 1.00a4    
02 Oct 2001 09:31:32
files touched by this commit
wjv search for other commits by this committer
- Update the included (optional) Biopython-CORBA pacakge to version 0.3.0   - If
CORBA support is included, the default ORB has changed from omniORB to     ORBit
  - PORTREVISION bump    
06 Sep 2001 13:42:36
files touched by this commit
wjv search for other commits by this committer
- Update to version 1.00.a3   - Use pkg-req to check the installed version of
Python    
09 Jul 2001 10:57:55
files touched by this commit
wjv search for other commits by this committer
Update to version 1.00.a2    
29 Jun 2001 16:04:07
files touched by this commit
wjv search for other commits by this committer
Use $FILESDIR rather than hard-coded path.    
15 Jun 2001 14:25:56
files touched by this commit
wjv search for other commits by this committer
Update to 1.00.a1; change MAINTAINER to my new address.   Many changes to port,
including addition of CORBA functionality.    
29 May 2001 13:50:08
files touched by this commit
sobomax search for other commits by this committer
math/numpy was renamed to math/py-numeric.    
08 Oct 2000 00:23:30
files touched by this commit
asami search for other commits by this committer
Convert category biology to new layout.  
11 Sep 2000 15:56:37
files touched by this commit
nbm search for other commits by this committer
Update to 0.90.d03    
08 Sep 2000 13:24:00
files touched by this commit
tg search for other commits by this committer
Don't break package building on Satoshi's cluster. Explicitly depend   on
python1.5:lang/python15.    
05 Aug 2000 17:01:27
files touched by this commit
will search for other commits by this committer
Upgrade to 0.90.d02.    
31 Jul 2000 13:12:24
files touched by this commit
nbm search for other commits by this committer
Add py-biopython, is a collection of Python packages and modules created   by
the Biopython Project, intended to provide the basis for building  
bioinformatics applications in the Python language.    

Number of commits found: 49

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