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Port details
emboss 6.6.0 biology on this many watch lists=2 search for ports that depend on this port
Collection of open source tools for genetic sequence analysis
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 31 Jul 2000 16:13:54
License: GPLv2


The European Molecular Biology Open Software Suite (EMBOSS) is a
comprehensive set (about 100) of open source tools for genetic sequence
analysis.  EMBOSS is produced by the European Molecular Biology Network
(EMBnet - http://www.embnet.org/).

All EMBOSS tools are all built around the same set of core libraries - AJAX
and NUCLEUS - and therefore share a unified user interface, have similar
"look and feel", and implement a uniform sequence addressing methodology.

The various components of EMBOSS are distributed under the GPL, except the
core libraries which are under the LGPL.

EMBASSY packages are third party applications which have been integrated with
the EMBOSS suite, but which are not included in the base EMBOSS distribution
for licensing or other reasons. The EMBASSY packages live in the
biology/embassy port. 

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

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

Required To Build:
  1. biology/clustalw
  2. biology/primer3
  3. devel/gmake
  4. x11/libX11
  5. x11/libXpm
Required To Run:
  1. x11/libX11
  2. x11/libXpm
Required Libraries:
  1. graphics/gd
  2. graphics/png
  3. graphics/gd
  4. graphics/png
  5. converters/libiconv
  6. x11-toolkits/open-motif

This port is required by:

for Libraries * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

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


Configuration Options
===> The following configuration options are available for emboss-6.6.0:
     DOCS=on: Build and/or install documentation
     X11=on: X11 (graphics) support
===> Use 'make config' to modify these settings

Master Sites:
  1. ftp://emboss.open-bio.org/pub/EMBOSS/
  2. http://distcache.FreeBSD.org/ports-distfiles/emboss/

Number of commits found: 82

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
09 Jun 2014 11:21:53
Original commit files touched by this commit  6.6.0
Revision:357139
olgeni search for other commits by this committer
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
05 Jun 2014 03:28:07
Original commit files touched by this commit  6.6.0
Revision:356575
miwi search for other commits by this committer
- Update to 6.6.0
- Stage support

PR:		190508
Submitted by:	Muhammad Moinur Rahman
05 May 2014 09:45:37
Original commit files touched by this commit  6.2.0_3
Revision:352986
bapt search for other commits by this committer
Convert all :U to :tu and :L to :tl

Since FreeBSD 8.4 and FreeBSD 9.1 make(1) do support :tu and :tl as a
replacement for :U and :L (which has been marked as deprecated)

bmake which is the default on FreeBSD 10+ only support by default
:tu/:tl a hack has been added at the time to support :U and :L to ease
migration. This hack is now not necessary anymore

Note that this makes the ports tree incompatible with make(1) from
FreeBSD 8.3 or earlier

With hat:	portmgr
11 Dec 2013 14:43:51
Original commit files touched by this commit  6.2.0_3
Revision:336171
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
20 Sep 2013 15:55:44
Original commit files touched by this commit  6.2.0_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)
09 Aug 2013 14:05:53
Refresh Original commit files touched by this commit
Revision:324437  Sanity Test Failure
dinoex search for other commits by this committer
- update libdg to 2.1.0
09 Jul 2013 21:49:36
Original commit files touched by this commit  6.2.0_2
Revision:322587
bapt search for other commits by this committer
Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake
01 Oct 2012 14:55:55
Original commit files touched by this commit  6.2.0_2
Revision:305131
wen search for other commits by this committer
- Take maintainership
01 Oct 2012 14:45:17
Original commit files touched by this commit  6.2.0_2
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
01 Jun 2012 05:26:28
Original commit files touched by this commit  6.2.0_2
dinoex search for other commits by this committer
- update png to 1.5.10
22 Oct 2011 23:50:23
Original commit files touched by this commit  6.2.0_1
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
02 Jul 2011 11:33:17
Original commit files touched by this commit  6.2.0_1
miwi search for other commits by this committer
- kick MD5
02 May 2011 12:44:53
Original commit files touched by this commit  6.2.0_1
makc search for other commits by this committer
Bump PORTREVISION after open-mofit update
04 Dec 2010 07:34:27
Original commit files touched by this commit  6.2.0
ade search for other commits by this committer
Sync to new bsd.autotools.mk
07 Apr 2010 01:16:50
Original commit files touched by this commit  6.2.0
wen search for other commits by this committer
- Update to 6.2.0

Submitted by:   Wen Heping(myself)
Approved by:    maintainer(via Email)
28 Mar 2010 06:47:48
Original commit files touched by this commit  6.0.1_3
dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
05 Feb 2010 11:46:55
Original commit files touched by this commit  6.0.1_2
dinoex search for other commits by this committer
- update to jpeg-8
14 Aug 2009 08:33:22
Original commit files touched by this commit  6.0.1_1
miwi search for other commits by this committer
- Update MASTER_SITES

PR:             137750
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
02 Aug 2009 19:36:34
Original commit files touched by this commit  6.0.1_1
mezz search for other commits by this committer
-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.

It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.

With help:      marcus and kwm
Pointyhat-exp:  a few times by pav
Tested by:      pgollucci, "Romain Tartière" <romain@blogreen.org>, and
                a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by:    marcus
Approved by:    portmgr
31 Jul 2009 13:57:52
Original commit files touched by this commit  6.0.1_1
dinoex search for other commits by this committer
- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin
14 Mar 2009 15:16:07
Original commit files touched by this commit  6.0.1
miwi search for other commits by this committer
- Force commit to correct the entry
- Update to 6.0.1

PR:             132504
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer
14 Mar 2009 15:14:45
Original commit files touched by this commit  6.0.1
miwi search for other commits by this committer
- Update to 0.1.24

PR:             132527
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer
17 Apr 2008 17:06:49
Original commit files touched by this commit  5.0.0
pav search for other commits by this committer
- Replace SF with second working master site

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
17 Apr 2008 01:31:23
Original commit files touched by this commit  5.0.0
rafan search for other commits by this committer
- It seems that upstream removes their distfiles from sourceforge, so add
  the download site pointed by their webpage as first choice.

Noticed by:    pointyhat via pav
13 Apr 2008 07:22:21
Original commit files touched by this commit  5.0.0
rafan search for other commits by this committer
- Update to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
13 Apr 2008 07:21:16
Original commit files touched by this commit  3.0.0_2
rafan search for other commits by this committer
- Sort pkg-plist before updating to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
23 Mar 2008 16:44:09
Original commit files touched by this commit  3.0.0_2
miwi search for other commits by this committer
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)
19 May 2007 20:32:57
Original commit files touched by this commit  3.0.0_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}.
31 Mar 2006 09:43:22
Original commit files touched by this commit  3.0.0
thierry search for other commits by this committer
For EMBOSS:

        This patch brings EMBOSS up to date with the current version.

        i.   The patches included in files/ are bugfixes for files in
             EMBOSS-3.0.0 that appeared after the release. They are
             documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

             This is just 'for the record' so that we remember to remove these
             patches in the next update.

        ii.  EMBOSS is now installed by default in LOCALBASE/emboss
             This is to avoid CONFLICTS with other ports that install files
             with the same names. Installing EMBOSS to another PREFIX is also
             possible.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
23 Feb 2006 10:40:45
Original commit files touched by this commit  2.10.0_1
ade search for other commits by this committer
Conversion to a single libtool environment.

Approved by:    portmgr (kris)
02 Feb 2006 23:12:05
Original commit files touched by this commit  2.10.0
marcus search for other commits by this committer
Remove CONFLICTS with nss.
22 Jan 2006 08:20:34
Original commit files touched by this commit  2.10.0
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
15 Nov 2005 06:52:12
Original commit files touched by this commit  2.10.0
ade search for other commits by this committer
Mass-conversion to the USE_AUTOTOOLS New World Order.  The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.

Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.

Preliminary documentation can be found at:
        http://people.FreeBSD.org/~ade/autotools.txt

which is in the process of being SGMLized before introduction into the
Porters Handbook.

Light blue touch-paper.  Run.
29 May 2005 18:26:05
Original commit files touched by this commit  2.10.0
pav search for other commits by this committer
- Update to 2.10.0

PR:             ports/81579
Submitted by:   "Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by:    Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
11 Feb 2005 21:11:51
Original commit files touched by this commit  2.9.0
sem search for other commits by this committer
- Add (or fix) CONFLICTS line. The ports install bin/digest.

Approved by:    portmgr (krion)
26 Nov 2004 01:11:43
Original commit files touched by this commit  2.9.0
sem search for other commits by this committer
- Update to 2.9.0
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
26 Nov 2004 00:25:38
Original commit files touched by this commit  2.4.1_3
kris search for other commits by this committer
Add missing files
20 Nov 2004 07:40:43
Original commit files touched by this commit  2.4.1_3
linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.
23 Jun 2004 08:20:21
Original commit files touched by this commit  2.4.1_3
vs search for other commits by this committer
Fix MASTER_SITES:
 - add trailing slash
 - ftp.ebi.ac.uk only has 2.8.0

PR:             ports/67427
Submitted by:   Roman Neuhauser
Approved by:    maintainer timeout
04 Feb 2004 05:21:48
Original commit files touched by this commit  2.4.1_3
marcus search for other commits by this committer
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)
20 Nov 2003 15:06:15
Original commit files touched by this commit  2.4.1_2
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  2.4.1_2
trevor search for other commits by this committer
Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.
18 Aug 2003 16:15:11
Original commit files touched by this commit  2.4.1_2
nork search for other commits by this committer
o Main modification
  graphics/gd(based on 1.8.4)    -> graphics/gd1
  graphics/gd2(based on 2.0.15)  -> graphics/gd
  graphics/p5-GD(based on 1.41)  -> graphics/p5-GD1
  graphics/p5-GD2(based on 2.07) -> graphics/p5-GD
  japanese/gd                    -> japanese/gd1
  japanese/gd2                   -> japanese/gd
o Include some feature
  WITH_XPM(w/, w/o WITHOUT_X11)
o Chase this modification
o Fix build error [1]

PR:             ports/54540
Submitted by:   Ports Fury
Approved by:    maintainer (blanket)
Reported by:    bento via kris [1]
08 Aug 2003 04:40:47
Original commit files touched by this commit  2.4.1_1
kris search for other commits by this committer
This port is scheduled for removal on Nov 7 2003 if it is still broken at
that time and no PRs have been submitted to fix it.  If you are interested
in saving this port, please send your patches to the maintainer.  If the
maintainer is unresponsive or the port has no maintainer, then please
submit them via send-pr.
07 Aug 2003 09:29:17
Original commit files touched by this commit  2.4.1_1
kris search for other commits by this committer
BROKEN: Checksum mismatch
11 Jul 2003 18:16:14
Original commit files touched by this commit  2.4.1_1
nork search for other commits by this committer
o Change library name from libgd to libgd1.
o Do not install everything except headers and libraries
  (to avoid conflicting with graphics/gd2)
o Fix dependency on new libgd1(for many ports).

PR:             ports/54100
Submitted by:   Ports Fury
07 Mar 2003 05:56:43
Original commit files touched by this commit  2.4.1
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.
27 Sep 2002 08:58:19
Original commit files touched by this commit  2.4.1
wjv search for other commits by this committer
- Unbreak fetching of distfiles.  (Needs update as soon as freeze is over.)

Submitted by:   kris, bento
Approved by:    Implicitly by first rule of ports freeze, I hope!
20 Sep 2002 20:45:20
Original commit files touched by this commit  2.4.1
kris search for other commits by this committer
BROKEN: Does not fetch
05 Jul 2002 10:09:32
Original commit files touched by this commit  2.4.1
wjv search for other commits by this committer
- Update to version 2.4.1
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)

PR:             40198 ; many private requests
Submitted by:   Tilman Linneweh <tilman@arved.de> (2.4.1 update)
17 May 2002 09:24:32
Original commit files touched by this commit  2.2.0
kris search for other commits by this committer
BROKEN: incorrect checksums
25 Mar 2002 09:19:21
Original commit files touched by this commit  2.2.0
sobomax search for other commits by this committer
Add USE_SUBMAKE, where it might be necessary.
18 Jan 2002 14:04:04
files touched by this commit
wjv search for other commits by this committer
- Update to version 2.2.0   - Update included EMBASSY package EMNU   - Fix a
long-standing bug in Makefile that would preclude PKGMESSAGE from     being
generated properly   - Consider this an interim update merely to track the
latest version - more     work is required to activate the newly included
"Jemboss" Java GUI     interface    
03 Aug 2001 12:32:42
files touched by this commit
wjv search for other commits by this committer
- Update port to version 2.0.1   - Add two new EMBASSY applications, MEME and
HMMER.    
11 Jul 2001 14:58:12
files touched by this commit
wjv search for other commits by this committer
Remove obsolete pointer to online documentation.    
11 Jul 2001 14:33:34
files touched by this commit
wjv search for other commits by this committer
Update package's URL; my email address.    
27 Jun 2001 11:15:02
files touched by this commit
wjv search for other commits by this committer
Updating my email address in my remaining ports.    
15 Jun 2001 13:11:33
files touched by this commit
wjv search for other commits by this committer
Update to 1.13.3; remove bogus file.    
30 May 2001 15:34:57
files touched by this commit
kevlo search for other commits by this committer
Update to version 1.13.1    
07 May 2001 13:18:58
files touched by this commit
jeh search for other commits by this committer
Update the EMBOSS suite (biology/emboss) to version 1.12.0    
12 Mar 2001 10:33:50
files touched by this commit
nbm search for other commits by this committer
Update the EMBOSS suite to v1.11.0    
28 Feb 2001 15:58:11
files touched by this commit
kevlo search for other commits by this committer
Update to version 1.10.1    
20 Feb 2001 15:51:34
files touched by this commit
kevlo search for other commits by this committer
Update to version 1.10.0    
12 Feb 2001 10:01:08
files touched by this commit
knu search for other commits by this committer
Chase graphics/gd's shlib version bump.    
29 Jan 2001 15:48:01
files touched by this commit
kevlo search for other commits by this committer
- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1   - Update the EMBASSY
package EMNU from 1.0.2 to 1.0.3   - Merged the four pkg-plist* files into one  
 
24 Jan 2001 11:36:38
files touched by this commit
kevlo search for other commits by this committer
Upgrade to version 1.9.0    
04 Dec 2000 13:00:08
files touched by this commit
roam search for other commits by this committer
Update distfiles' checksums after the distfiles have been rerolled yet   again
without changing names or versions.  Also add a new MASTER_SITE.    
30 Nov 2000 20:13:30
files touched by this commit
roam search for other commits by this committer
Distfile tarballs were rerolled without notice due to a minor bug.    
28 Nov 2000 01:43:40
files touched by this commit
jeh search for other commits by this committer
- Update port biology/emboss from 1.7.0 to 1.8.0    
19 Nov 2000 03:06:48
files touched by this commit
jeh search for other commits by this committer
Make nolonger support :U.  Fix to compensate for that.    
13 Nov 2000 13:49:46
files touched by this commit
jeh search for other commits by this committer
- This is a fairly extensive rework of this port.   - "EMBASSY" applications are
third party tools which have been adapted to     function as part of EMBOSS, but
which are not included with the base EMBOSS     distribution for licensing or
other reasons.  This new version of the     EMBOSS port now contains the three
current EMBASSY applications as well,     and during installation the user is
presented with a dialog(1) menu to    
13 Nov 2000 13:48:50
files touched by this commit
jeh search for other commits by this committer
- This is a fairly extensive rework of this port.   - "EMBASSY" applications are
third party tools which have been adapted to     function as part of EMBOSS, but
which are not included with the base EMBOSS     distribution for licensing or
other reasons.  This new version of the     EMBOSS port now contains the three
current EMBASSY applications as well,     and during installation the user is
presented with a dialog(1) menu to     choose which of these should be
isntalled.    
01 Nov 2000 11:54:56
files touched by this commit
jeh search for other commits by this committer
Make portlint happy, remove a space    
01 Nov 2000 11:49:08
files touched by this commit
jeh search for other commits by this committer
Update to version 1.7.0    
10 Oct 2000 05:54:36
files touched by this commit
kevlo search for other commits by this committer
- Update to 1.6.0   - Reorder packing list    
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.  
22 Sep 2000 11:24:52
files touched by this commit
kris search for other commits by this committer
Add USE_XLIB    
08 Sep 2000 11:07:13
files touched by this commit
nbm search for other commits by this committer
Upgrade to 1.5.0    
07 Sep 2000 15:02:53
files touched by this commit
nbm search for other commits by this committer
Update to emboss 1.4.0.    
21 Aug 2000 11:07:37
files touched by this commit
sobomax search for other commits by this committer
USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.    
12 Aug 2000 17:15:48
files touched by this commit
nbm search for other commits by this committer
Update to emboss 1.1.0, fixing some style bugs too.    
31 Jul 2000 20:13:54
files touched by this commit
nbm search for other commits by this committer
Add emboss, the European Molecular Biology Open Software Suite    

Number of commits found: 82

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