embassy 5.0.0 biology =0

A collection of contributed EMBOSS applications
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 26 Nov 2004 16:35:20

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EMBASSY is a collection of contributed EMBOSS software. From the web
pages:

 "EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL).
 Programs which have been included from third parties who have their own
 licencing terms are kept apart under the EMBASSY grouping.

 This allows the EMBOSS libraries to link to other software, and only
 requires that software to have an LGPL-compatible licence. Phylip, for
 example, fits this model.

 But, to the user they do look exactly like EMBOSS aplications."

WWW: http://emboss.sourceforge.net/apps/#Embassy

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

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Required To Build: devel/gmake, x11/libX11, x11/libXpm
Required To Run: x11/libX11, x11/libXpm
Required Libraries: biology/emboss, converters/libiconv, x11-toolkits/open-motif

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

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Configuration Options

===> The following configuration options are available for embassy-5.0.0:
     DOMAINATRIX=on (default) "Protein domain apps"
     DOMALIGN=on (default) "Protein domain apps"
     DOMSEARCH=on (default) "Protein domain apps"
     SIGNATURE=on (default) "Protein domain apps"
     STRUCTURE=on (default) "Protein domain apps"
     EMNU=on (default) "EMBOSS simple menu"
     ESIM4=on (default) "Align cDNA/EST to genome"
     HMMER=on (default) "HMM alignment and searches"
     MEME=on (default) "Motif detection"
     MSE=on (default) "A multiple sequence screen editor"
     MYEMBOSS=on (default) "Examples for developers of EMBOSS apps"
     PHYLIP=on (default) "Phylogeny inference"
     TOPO=on (default) "Transmembrane display"
     VIENNA=on (default) "RNA folding"
===> Use 'make config' to modify these settings

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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.
  
  

- Update to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan at 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}.

- Fix after objformat removal

Reported by:    pointyhat

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.

Add missing USE_ICONV

SHA256ify

Approved by:    krion@

- Update to 2.10.0

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

- Fix OPTIONS handling

Pointy hat to:  sem

BROKEN: Broken distinfo file

[new port] biology/embassy

PR:             ports/74330
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>

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

^* - modified, not new

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