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Port details
biojava 1.7,1 biology on this many watch lists=2 search for ports that depend on this port
Open-source Java tools for processing biological data
Maintained by: wenheping@gmail.com search for ports maintained by this maintainer
Port Added: 10 Oct 2000 08:14:04
Also Listed In: java
License: not specified in port


The BioJava Project is an open-source project dedicated to providing Java
tools for processing biological data. This will include objects for
manipulating sequences, file parsers, CORBA interoperability, access to
ACeDB, dynamic programming, and simple statistical routines. 

The BioJava library is useful for automating those daily and mundane
bioinformatics tasks. As the library matures, the BioJava libraries will
provide a foundation upon which both free software and commercial packages
can be developed.

WWW: http://www.biojava.org/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

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

Required To Build:
  1. java/openjdk6
  2. devel/apache-ant
Required To Run:
  1. java/openjdk6
There are no ports dependent upon this port

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


Configuration Options
===> The following configuration options are available for biojava-1.7,1:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/
  2. http://www.biojava.org/download/bj17/all/

Number of commits found: 34

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
01 Jun 2014 10:37:23
Original commit files touched by this commit  1.7,1
Revision:356092
ohauer search for other commits by this committer
- add stage support
08 Mar 2014 16:39:01
Original commit files touched by this commit  1.7,1
Revision:347521
antoine search for other commits by this committer
Unbreak
07 Mar 2014 15:52:40
Original commit files touched by this commit  1.7,1
Revision:347402
bapt search for other commits by this committer
Convert b* to USES=zip
21 Feb 2014 13:35:26
Original commit files touched by this commit  1.7,1
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  1.7,1
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
03 Jan 2014 15:46:52
Original commit files touched by this commit  1.7,1
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.7,1
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)
11 Dec 2012 07:26:39
Original commit files touched by this commit  1.7,1
Revision:308665
bapt search for other commits by this committer
Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIP
instead given that jar files are just zip files, remove hardcoded do extract
target.

Reported by:	linimon, matthew
10 Dec 2012 13:18:29
Original commit files touched by this commit  1.7,1
Revision:308604
bapt search for other commits by this committer
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to JAVA_VERSION=	1.5+ (part2)
29 Jul 2012 11:17:04
Original commit files touched by this commit  1.7,1
cs search for other commits by this committer
Fix typos in COMMENT

Approved by:	portmgr@ (implicit)
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.7,1
miwi search for other commits by this committer
- Get Rid MD5 support
01 May 2009 09:33:42
Original commit files touched by this commit  1.7,1
miwi search for other commits by this committer
- Update to 1.7
- Pass maintainership to submitter

PR:             134056
Submitted by:   Wen Heping <wenheping@gmail.com>
08 Dec 2008 06:43:50
Original commit files touched by this commit  1.5.b2_2,1
linimon search for other commits by this committer
Reset nemoliu due to maintainer-timeouts and no response to email.

Hat:    portmgr
06 Jun 2008 13:08:29
Original commit files touched by this commit  1.5.b2_2,1
edwin search for other commits by this committer
Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)
19 May 2007 20:32:57
Original commit files touched by this commit  1.5.b2_1,1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
30 Apr 2007 06:27:41
Original commit files touched by this commit  1.5.b2,1
nemoliu search for other commits by this committer
Use my @FreeBSD.org address.

Approved by:    delphij (mentor)
27 Mar 2007 08:01:54
Original commit files touched by this commit  1.5.b2,1
miwi search for other commits by this committer
- Update to 1.5-beta2
- Pass maintainership to submitter

PR:             110621
Submitted by:   Nemo Liu<nemoliu@gmail.com>
11 Feb 2007 01:23:35
Original commit files touched by this commit  1.5.b,1
kris search for other commits by this committer
Schedule these broken ports for removal on 2007-04-10 if they are still
broken at that time and no fix has been submitted.
05 Feb 2007 00:08:52
Original commit files touched by this commit  1.5.b,1
kris search for other commits by this committer
BROKEN: Does not build
13 Dec 2006 12:56:01
Original commit files touched by this commit  1.5.b,1
linimon search for other commits by this committer
Reset whitekid@gmail.com after timeouts and no response to email.

Hat:            portmgr
21 Nov 2006 22:35:28
Original commit files touched by this commit  1.5.b,1
thierry search for other commits by this committer
- Upgrade to the latest beta and unbreak;

- Add a regression-test target;

- Fix plist for WITHOUT_SAMPLES.

PR:             ports/104685
Approved by:    maintainer's time-out (1 month)
02 Sep 2006 16:51:10
Original commit files touched by this commit  1.30
kris search for other commits by this committer
Schedule these broken ports for termination on 2006-12-01
22 Apr 2006 22:09:45
Original commit files touched by this commit  1.30
kris search for other commits by this committer
BROKEN: Does not compile
22 Jan 2006 08:20:34
Original commit files touched by this commit  1.30
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
22 Nov 2004 15:47:58
Original commit files touched by this commit  1.30
vs search for other commits by this committer
- Update biology/biojava to 1.30
- Install javadoc and example files
- Assign maintainership to submitter

PR:             ports/73391
Submitted by:   Cheng-Dae Choe
Add. reviewing: hq@
27 Jan 2004 20:51:07
Original commit files touched by this commit  1.01
trevor search for other commits by this committer
Add SIZE.
02 Nov 2003 02:48:09
Original commit files touched by this commit  1.01
edwin search for other commits by this committer
ports with possibly unreachable MAINTAINERs
*** addresses that seem to be dead:

PR:             ports/58694
Submitted by:   Oliver Eikemeier <eikemeier@fillmore-labs.com>
22 Oct 2003 09:29:55
Original commit files touched by this commit  1.01
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
19 Oct 2003 02:26:52
Original commit files touched by this commit  1.01
kris search for other commits by this committer
Don't remove share/java/classes system directory.
21 Feb 2003 11:01:38
Original commit files touched by this commit  1.01
knu search for other commits by this committer
De-pkg-comment.
16 Jun 2002 01:08:49
Original commit files touched by this commit  1.01
glewis search for other commits by this committer
Unbreak this port:

. Fix dependencies to be in sync with the recent JDK ports renaming.
. Replace MASTER_SITES with a location that actually contains the
  source.
. Fix the packing list.

Note that there is a much newer version of this application available,
but that is beyond the scope of what I was trying to do (just fix the
JDK dependency), as is the last two items.
20 Nov 2001 23:29:38
files touched by this commit
lioux search for other commits by this committer
Style police: WWW tags should either end in a file/script or TRAILING /; Fix the
later case    
08 Jul 2001 19:15:34
files touched by this commit
ijliao search for other commits by this committer
Add NOPORTDOCS support to pkg-plist    
10 Oct 2000 12:14:04
files touched by this commit
jeh search for other commits by this committer
Initial import of biology/biojava    

Number of commits found: 34

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