The FreeBSD Ports Archive

FreeBSD biology : emboss

A collection of open source tools for genetic sequence analysis

 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.  This port includes the currently available
EMBASSY applications.  During an interactive install the user will be asked
to choose which of these will be installed (default: all).  Note that the
EMBASSY versions of PHYLIP and HMMER should not clash with the standalone
versions (also in ports/biology) due to the fact that their binaries have been
renamed. 

emboss history

v. 1.48
date: 2007/05/19 20:00:23;  author: flz;  state: Exp;  lines: +1 -0
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

v. 1.47
date: 2006/03/31 09:43:20;  author: thierry;  state: Exp;  lines: +15 -14
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.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero  (maintainer)

v. 1.46
date: 2006/02/23 10:34:51;  author: ade;  state: Exp;  lines: +1 -1
Conversion to a single libtool environment.

Approved by:	portmgr (kris)

v. 1.45
date: 2006/02/02 23:12:04;  author: marcus;  state: Exp;  lines: +1 -1
Remove CONFLICTS with nss.

v. 1.44
date: 2005/11/15 06:48:10;  author: ade;  state: Exp;  lines: +1 -1
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.

v. 1.43
date: 2005/05/29 18:26:05;  author: pav;  state: Exp;  lines: +1 -1
- Update to 2.10.0

PR:		ports/81579
Submitted by:	"Choe, Cheng-Dae" 
Approved by:	Fernan Aguero  (maintainer)

v. 1.42
date: 2005/02/11 21:11:51;  author: sem;  state: Exp;  lines: +2 -0
- Add (or fix) CONFLICTS line. The ports install bin/digest.

Approved by:	portmgr (krion)

v. 1.41
date: 2004/11/26 01:11:42;  author: sem;  state: Exp;  lines: +23 -105
- Update to 2.9.0
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero 

v. 1.40
date: 2004/11/20 07:40:43;  author: linimon;  state: Exp;  lines: +1 -1
With portmgr hat on, reset inactive maintainer.

v. 1.39
date: 2004/06/23 08:20:21;  author: vs;  state: Exp;  lines: +2 -2
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

v. 1.38
date: 2004/02/04 05:18:49;  author: marcus;  state: Exp;  lines: +1 -1
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)

v. 1.37
date: 2003/11/20 15:05:56;  author: trevor;  state: Exp;  lines: +1 -1
Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:	Oliver Eikemeier

v. 1.36
date: 2003/11/20 13:51:33;  author: trevor;  state: Exp;  lines: +1 -0
Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.

v. 1.35
date: 2003/08/18 16:15:05;  author: nork;  state: Exp;  lines: +4 -6
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]

v. 1.34
date: 2003/08/08 04:40:38;  author: kris;  state: Exp;  lines: +0 -0
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.

v. 1.33
date: 2003/08/07 09:29:17;  author: kris;  state: Exp;  lines: +2 -0
BROKEN: Checksum mismatch

v. 1.32
date: 2003/07/11 18:16:11;  author: nork;  state: Exp;  lines: +2 -1
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

v. 1.31
date: 2003/03/07 05:56:41;  author: ade;  state: Exp;  lines: +1 -0
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

v. 1.30
date: 2002/09/27 08:58:19;  author: wjv;  state: Exp;  lines: +1 -3
- 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!

v. 1.29
date: 2002/09/20 20:45:20;  author: kris;  state: Exp;  lines: +2 -0
BROKEN: Does not fetch

v. 1.28
date: 2002/07/05 10:09:31;  author: wjv;  state: Exp;  lines: +23 -9
- 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  (2.4.1 update)

v. 1.27
date: 2002/05/17 09:24:32;  author: kris;  state: Exp;  lines: +2 -0
BROKEN: incorrect checksums

v. 1.26
date: 2002/03/25 09:19:17;  author: sobomax;  state: Exp;  lines: +1 -0
Add USE_SUBMAKE, where it might be necessary.

v. 1.25
date: 2002/01/18 14:04:03;  author: wjv;  state: Exp;  lines: +5 -6
- 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

v. 1.24
date: 2001/08/03 11:32:41;  author: wjv;  state: Exp;  lines: +6 -3
- Update port to version 2.0.1
- Add two new EMBASSY applications, MEME and HMMER.

v. 1.23
date: 2001/06/27 10:14:47;  author: wjv;  state: Exp;  lines: +2 -2
Updating my email address in my remaining ports.

Prompted by:	vanilla

v. 1.22
date: 2001/06/15 12:11:33;  author: wjv;  state: Exp;  lines: +2 -2
Update to 1.13.3; remove bogus file.

PR:		28119
Reviewed by:	nbm

v. 1.21
date: 2001/05/30 14:34:48;  author: kevlo;  state: Exp;  lines: +4 -4
Update to version 1.13.1

PR: 27768
Submitted by: MAINTAINER

v. 1.20
date: 2001/05/07 12:18:57;  author: jeh;  state: Exp;  lines: +2 -2
Update the EMBOSS suite (biology/emboss) to version 1.12.0

PR:		27179
Submitted by:	Johann Visagie  MAINTAINER

v. 1.19
date: 2001/03/12 10:33:50;  author: nbm;  state: Exp;  lines: +3 -4
Update the EMBOSS suite to v1.11.0

PR:		25728
Submitted by:	johann@egenetics.com

v. 1.18
date: 2001/02/28 15:58:11;  author: kevlo;  state: Exp;  lines: +2 -2
Update to version 1.10.1

PR: 25449
Submitted by: maintainer

v. 1.17
date: 2001/02/20 15:51:29;  author: kevlo;  state: Exp;  lines: +7 -5
Update to version 1.10.0

PR: 25228
Submitted by: MAINTAINER

v. 1.16
date: 2001/02/12 10:01:01;  author: knu;  state: Exp;  lines: +3 -2
Chase graphics/gd's shlib version bump.

v. 1.15
date: 2001/01/29 15:47:57;  author: kevlo;  state: Exp;  lines: +12 -14
- 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

PR: 24717
Submitted by: MAINTAINER

v. 1.14
date: 2001/01/24 11:36:35;  author: kevlo;  state: Exp;  lines: +7 -5
Upgrade to version 1.9.0

PR: 24597
Submitted by: MAINTAINER

v. 1.13
date: 2000/12/04 13:00:07;  author: roam;  state: Exp;  lines: +3 -2
Update distfiles' checksums after the distfiles have been rerolled yet
again without changing names or versions.  Also add a new MASTER_SITE.

PR:		23262
Submitted by:	Johann Visagie 

v. 1.12
date: 2000/11/28 01:43:39;  author: jeh;  state: Exp;  lines: +8 -9
- Update port biology/emboss from 1.7.0 to 1.8.0

PR:		23130
Submitted by:	Johann Visagie  MAINTAINER

v. 1.11
date: 2000/11/19 03:06:48;  author: jeh;  state: Exp;  lines: +7 -4
Make nolonger support :U.  Fix to compensate for that.

Submitted by:	fenner
Approved by:	MAINTAINER

v. 1.10
date: 2000/11/13 13:48:48;  author: jeh;  state: Exp;  lines: +75 -3
- 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.

PR:		22818
Submitted by:	Johann Visagie  MAINTAINER

v. 1.9
date: 2000/11/01 11:54:56;  author: jeh;  state: Exp;  lines: +2 -2
Make portlint happy, remove a space

v. 1.8
date: 2000/11/01 11:49:07;  author: jeh;  state: Exp;  lines: +2 -2
Update to version 1.7.0

PR:		22474
Submitted by:	Johann Visagie  MAINTAINER

v. 1.7
date: 2000/10/10 04:54:35;  author: kevlo;  state: Exp;  lines: +2 -2
- Update to 1.6.0
- Reorder packing list

PR: 21857
Submitted by: MAINTAINER

v. 1.6
date: 2000/09/22 10:24:52;  author: kris;  state: Exp;  lines: +2 -1
Add USE_XLIB

v. 1.5
date: 2000/09/08 10:07:11;  author: nbm;  state: Exp;  lines: +4 -3
Upgrade to 1.5.0

PR:		21108
Submitted by:	Johann Visagie 

v. 1.4
date: 2000/09/07 14:02:51;  author: nbm;  state: Exp;  lines: +11 -11
Update to emboss 1.4.0.

PR:		ports/20898
Submitted by:	Johann Visagie 

v. 1.3
date: 2000/08/21 10:07:20;  author: sobomax;  state: Exp;  lines: +1 -2
USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.

v. 1.2
date: 2000/08/12 16:15:47;  author: nbm;  state: Exp;  lines: +18 -2
Update to emboss 1.1.0, fixing some style bugs too.

PR:		ports/20519
Submitted by:	Johann Visagie  (maintainer)

v. 1.1
date: 2000/07/31 19:13:53;  author: nbm;  state: Exp;
Add emboss, the European Molecular Biology Open Software Suite

PR:		ports/20317
Submitted by:	Johann Visagie 
=============================================================================