acacemic/EMBASSY: Updated for version 6.5.7.

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

1 files changed, 46 insertions, 76 deletions

diff --git a/academic/EMBASSY/CONTENTS b/academic/EMBASSY/CONTENTS
index d739dcfb711e..bd0665b82b44 100644
--- a/academic/EMBASSY/CONTENTS
+++ b/academic/EMBASSY/CONTENTS
@@ -1,94 +1,64 @@
-The EMBASSY package includes the following:
--------------------------------------------
+CBSTOOLS: The CBSTOOLS package is a set of wrappers to selected
+applications from the CBS group in Denmark.
 
-DOMAINATRIX Previous distributions of the protein domain programs from
-Jon Ison's group were in a single EMBASSY package. This is now split
-into 5 packages according to function.
+CLUSTALOMEGA: A wrapper for the clustal omega application.
 
-Application details and documentation for DOMAINATRIX
+DOMAINATRIX: The DOMAINATRIX programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-DOMAINATRIX is available as a Beta release 0.1.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMAINATRIX-0.1.0.tar.gz
+DOMALIGN: The DOMALIGN programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-Application details and documentation for DOMALIGN
+DOMSEARCH: The DOMSEARCH programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-DOMALIGN is available as a Beta release 0.1.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMALIGN-0.1.0.tar.gz
+EMNU: The EMNU package is a simple EMBOSS menu system written by Gary
+Williams at HGMP.
 
-Application details and documentation for DOMSEARCH
+ESIM4: The ESIM4 package is an EMBOSS conversion of the SIM4 package
+from Liliana Florea.
 
-DOMSEARCH is available as a Beta release 0.1.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMSEARCH-0.1.0.tar.gz
+HMMER: A suite of application wrappers to the original hmmer v2.3.2
+applications written by Sean Eddy. hmmer v2.3.2 must be installed on
+the same system as EMBOSS and the location of the hmmer executables
+must be defined in your path for EMBASSY HMMER to work.
 
-Application details and documentation for SIGNATURE
+IPRSCAN: The IPRSCAN package is a wrapper for the interproscan
+program.
 
-SIGNATURE is available as a Beta release 0.1.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file SIGNATURE-0.1.0.tar.gz
+MEME: The EMBASSY MEME package contains 'wrapper' applications
+providing an EMBOSS-style interface to the applications in the
+original MEME package version 4.0.0 developed by Timothy L. Bailey.
 
-Application details and documentation for STRUCTURE
+MIRA: The MIRA package is a fragment assembly program from Bastien
+Chevreux. The program was converted to EMBOSS by Alan Bleasby as two
+applications, one for EST assembly and one for shotgun fragment
+assembly
 
-STRUCTURE is available as a Beta release 0.1.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file STRUCTURE-0.1.0.tar.gz EMNU
-(EMBOSS Menu is Not UNIX) Application details and documentation for EMNU
+MSE: The MSE package is a multiple sequence editor. The program was
+contributed to the EMBOSS package by the author, Will Gilbert, as one
+of the first EMBASSY programs.
 
-EMNU is available as release 1.05 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file EMNU-1.05.tar.gz ESIM4
-(EMBOSS version of SIM4) Application details and documentation for ESIM4
+MYEMBOSS: A package for your own software developments.
 
-ESIM4 is available as release 1.0.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file ESIM4-1.0.0.tar.gz HMMER
-(EMBOSS version of HMMER 2.1.1 - PLEASE USE HMMERNEW) Application details
-and documentation for HMMER
+MYEMBOSSDEMO: The MYEMBOSSDEMO package contains example applications
+using EMBOSS data types
 
-HMMER is available as release 2.1.1 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.1.1.tar.gz HMMERNEW
-(EMBOSS version of HMMER 2.3.2) Application details and documentation
-for HMMERNEW
+PHYLIPNEW: The PHYLIPNEW programs are EMBOSS conversions of the
+programs in Joe Felsenstein's PHYLIP package, version 3.69.
 
-HMMER 2.3.2 is available from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.3.2.tar.gz
-MEME (previous EMBOSS version of MEME 2.3.1) Application details and
-documentation for MEME
+SIGNATURE: The SIGNATURE programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-MEME is available as release 2.3.1 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEME-2.3.1.tar.gz MEMENEW
-(EMBOSS version of MEME 3.0.14) Application details and documentation
-for MEMENEW which wraps release 3.0.14 of the Meme package
+STRUCTURE: The STRUCTURE programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-MEMENEW is available as release 0.1.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEMENEW-0.1.0.tar.gz
-MSE (A Multiple Sequence Screen Editor for Biological Sequences.)
-Application details and documentation for MSE
+TOPO: The TOPO package is a graphics program to display membrane
+protein topology by Susan Jean Johns.
 
-MSE is available as release 1.0.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file MSE-1.0.0.tar.gz MYEMBOSS
-(For sites to build their own applications) Application details and
-documentation for MYEMBOSS
-
-MYEMBOSS provides a directory structure and makefile stubs for developing
-your own applications more easily than in versions before 3.0.0.
-
-MYEMBOSS requires autoconf, automake and libtool to be installed. See
-the INSTALL file for more informations.
-
-MYEMBOSS is available as release 1.0.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file MYEMBOSS-1.0.0.tar.gz PHYLIP
-(Phylogeny Inference Package) Application details and documentation for
-PHYLIP and PHYLIPNEW.
-
-PHYLIP 3.572 was available as an EMBASSY package with previous
-releases. From 3.0.0 we are including a beta test conversion of PHYLIP
-3.61 (PHYLIPNEW). Program names now begin with 'f' rather than 'e'
-and interfaces are more EMBOSS-like. Please pass on feedback to our bug
-reporting list emboss-bug@emboss.open-bio.org
-
-PHYLIPNEW is available as a Beta release 3.6b from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIP-3.6b.tar.gz TOPO
-(Transmembrane display) Application details and documentation for TOPO
-
-TOPO is available as release 1.0.0 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file TOPO-1.0.0.tar.gz Vienna
-RNA package Application details and documentation for VIENNA
-
-Vienna is available as release 1.6 from our FTP server
-ftp://emboss.open-bio.org/pub/EMBOSS/ in file VIENNA-1.6.tar.gz
+VIENNA: These programs are adapted from the VIENNA RNA package.