academic/staden: Several fixes/enhancements

I notified upstream that Staden had been added to SlackBuilds.org
and got some handy tips. So:

1) The components of the program will now find their documentation
   directly.
2) The Staden package is now ready to provide a GUI for EMBOSS.
3) The real icons are used (converted from their Mac format).

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

1 files changed, 20 insertions, 16 deletions

diff --git a/academic/staden/README b/academic/staden/README
index 58460934c6..ccb3223dcf 100644
--- a/academic/staden/README
+++ b/academic/staden/README
@@ -2,26 +2,30 @@ The programs part of the Staden package provide a fully developed set
 of DNA sequence assembly, editing, analysis and more.
 
 Some of its features include:
-GAP4 - Performs assembly, contig joining, assembly checking, repeat search,
-       experiment suggestion, read pair analysis and contig editing.
-GAP5 - The new development version of Gap4, designed to work with the large
-       volumes of data attainable through the newer sequencing technologies.
-PREGAP4 - Provides a graphical user interface to set up the processing 
-          required to prepare trace data for assembly or analysis. 
-SPIN - Compares pairs of sequences in many ways, often presenting its results
-       graphically and has a sliding sequence window linked to the plots.
-TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF trace files.
+GAP4 - Performs assembly, contig joining, assembly checking, repeat
+       search, experiment suggestion, read pair analysis and contig
+       editing.
+GAP5 - The new development version of Gap4, designed to work with the
+       large volumes of data attainable through the newer sequencing
+       technologies.
+PREGAP4 - Provides a graphical user interface to set up the processing
+          required to prepare trace data for assembly or analysis.
+SPIN - Compares pairs of sequences in many ways, often presenting its
+       results graphically and has a sliding sequence window linked to
+       the plots.
+TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF
+       trace files.
 
-For more information and citing, visit Staden's web page and check the 
+For more information and citing, visit Staden's web page and check the
 "References" file in the documentation.
 
 This requires io_lib and tklib.
 
 Notes:
 1) You should run the SlackBuild in real root environment (su -)!
-2) Make sure you have Emacs and Tetex installed, as they are needed
-   to generate the documentation.
-3) Slackware's TCL and TK sources are expected to be in /tmp at build
-   time. The SlackBuild will unpack them in the build directory and
-   create the necessary symlinks in /tmp. You can safely delete the
-   symlinks when the build is complete.
+2) Make sure you have Emacs and Tetex installed at build time.
+3) Although unsupported at the moment, SPIN can provide a GUI for the
+   EMBOSS suite programs. If you want to give it a try, run as root
+   "create_emboss_data" (EMBOSS should be installed, of course). This
+   generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl,
+   so remember to manually clean them if you later uninstall staden.