emboss 5.0.0 biology =3

A collection of open source tools for genetic sequence analysis
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 31 Jul 2000 17:13:54

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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/

-- Johann Visagie <wjv@FreeBSD.org>

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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Required To Build: biology/clustalw, biology/primer3, devel/gmake, x11/libX11, x11/libXpm, devel/libtool15
Required To Run: x11/libX11, x11/libXpm
Required Libraries: graphics/gd, graphics/png, graphics/gd, graphics/png, x11-toolkits/open-motif

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

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Configuration Options

     No options to configure

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Master Sites:

ftp://emboss.open-bio.org/pub/EMBOSS/

ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/emboss/

• 2006-03-31

  Affects: users of biology/emboss and biology/embassy

  Author: fernan@iib.unsam.edu.ar

  Reason: 
    Since EMBOSS-3.0.0 both EMBOSS and EMBASSY install by default into
    $LOCALBASE/emboss to avoid conflicts with other ports.
  
    Users upgrading to 3.0.0 should take this into consideration when
    planning the upgrade, because it will involve moving data not
    installed by the port (databases) and tweaking the emboss.defaults
    config file.
  
    If you want to install the ports into $LOCALBASE (/usr/local, the old
    behavior), you can still do so by setting PREFIX manually. But you
    will have to take care of conflicting ports yourself.
  
  

- Replace SF with second working master site

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- 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

- Update to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)

- Sort pkg-plist before updating to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

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.

Conversion to a single libtool environment.

Approved by:    portmgr (kris)

Remove CONFLICTS with nss.

SHA256ify

Approved by:    krion@

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.

- 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)

- Add (or fix) CONFLICTS line. The ports install bin/digest.

Approved by:    portmgr (krion)

- Update to 2.9.0
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>

Add missing files

With portmgr hat on, reset inactive maintainer.

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

Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)

Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:   Oliver Eikemeier

Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.

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]

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.

BROKEN: Checksum mismatch

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

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

- 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!

BROKEN: Does not fetch

- 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)

BROKEN: incorrect checksums

Add USE_SUBMAKE, where it might be necessary.

- 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    

- Update port to version 2.0.1   - Add two new EMBASSY applications, MEME and
HMMER.    

Remove obsolete pointer to online documentation.    

Update package's URL; my email address.    

Updating my email address in my remaining ports.    

Update to 1.13.3; remove bogus file.    

Update to version 1.13.1    

Update the EMBOSS suite (biology/emboss) to version 1.12.0    

Update the EMBOSS suite to v1.11.0    

Update to version 1.10.1    

Update to version 1.10.0    

Chase graphics/gd's shlib version bump.    

- 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  
 

Upgrade to version 1.9.0    

Update distfiles' checksums after the distfiles have been rerolled yet   again
without changing names or versions.  Also add a new MASTER_SITE.    

Distfile tarballs were rerolled without notice due to a minor bug.    

- Update port biology/emboss from 1.7.0 to 1.8.0    

Make nolonger support :U.  Fix to compensate for that.    

- 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    

- 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.    

Make portlint happy, remove a space    

Update to version 1.7.0    

- Update to 1.6.0   - Reorder packing list    

Convert category biology to new layout.  

Add USE_XLIB    

Upgrade to 1.5.0    

Update to emboss 1.4.0.    

USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.    

Update to emboss 1.1.0, fixing some style bugs too.    

Add emboss, the European Molecular Biology Open Software Suite    

10 vulnerabilities affecting 29 ports have been reported in the past 14 days

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