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>

13 files changed, 42 insertions, 31 deletions

diff --git a/academic/staden/README b/academic/staden/README
index 58460934c6a3d..ccb3223dcfe39 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.
diff --git a/academic/staden/desktop/gap4.desktop b/academic/staden/desktop/gap4.desktop
index 1a07a8a378ad2..e0200a38d59fb 100644
--- a/academic/staden/desktop/gap4.desktop
+++ b/academic/staden/desktop/gap4.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=Education;
 Exec=gap4
-Icon=staden
+Icon=gap4
 Name=Staden Package GAP4
 StartupNotify=false
 Type=Application
diff --git a/academic/staden/desktop/gap4.png b/academic/staden/desktop/gap4.png
new file mode 100644
index 0000000000000..98248c7517a0f
--- /dev/null
+++ b/academic/staden/desktop/gap4.png
diff --git a/academic/staden/desktop/gap5.desktop b/academic/staden/desktop/gap5.desktop
index 383388c8bbd18..1901860d3feda 100644
--- a/academic/staden/desktop/gap5.desktop
+++ b/academic/staden/desktop/gap5.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=Education;
 Exec=gap5
-Icon=staden
+Icon=gap5
 Name=Staden Package GAP5
 StartupNotify=false
 Type=Application
diff --git a/academic/staden/desktop/gap5.png b/academic/staden/desktop/gap5.png
new file mode 100644
index 0000000000000..98248c7517a0f
--- /dev/null
+++ b/academic/staden/desktop/gap5.png
diff --git a/academic/staden/desktop/pregap4.desktop b/academic/staden/desktop/pregap4.desktop
index 645cf11968f6b..df13c9366ea7f 100644
--- a/academic/staden/desktop/pregap4.desktop
+++ b/academic/staden/desktop/pregap4.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=Education;
 Exec=pregap4
-Icon=staden
+Icon=pregap4
 Name=Staden Package PREGAP4
 StartupNotify=false
 Type=Application
diff --git a/academic/staden/desktop/pregap4.png b/academic/staden/desktop/pregap4.png
new file mode 100644
index 0000000000000..ad7fbbbe9a0a1
--- /dev/null
+++ b/academic/staden/desktop/pregap4.png
diff --git a/academic/staden/desktop/spin.desktop b/academic/staden/desktop/spin.desktop
index b220336034e72..8a9f14926a795 100644
--- a/academic/staden/desktop/spin.desktop
+++ b/academic/staden/desktop/spin.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=Education;
 Exec=spin
-Icon=staden
+Icon=spin
 Name=Staden Package SPIN
 StartupNotify=false
 Type=Application
diff --git a/academic/staden/desktop/spin.png b/academic/staden/desktop/spin.png
new file mode 100644
index 0000000000000..ad7fbbbe9a0a1
--- /dev/null
+++ b/academic/staden/desktop/spin.png
diff --git a/academic/staden/desktop/trev.desktop b/academic/staden/desktop/trev.desktop
index cc620d24c5d7b..45fa67bce1083 100644
--- a/academic/staden/desktop/trev.desktop
+++ b/academic/staden/desktop/trev.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=Education;
 Exec=trev
-Icon=staden
+Icon=trev
 Name=Staden Package TREV
 StartupNotify=false
 Type=Application
diff --git a/academic/staden/desktop/trev.png b/academic/staden/desktop/trev.png
new file mode 100644
index 0000000000000..c7ae77a0f2192
--- /dev/null
+++ b/academic/staden/desktop/trev.png
diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild
index a950d643efb32..707e9007deec0 100644
--- a/academic/staden/staden.SlackBuild
+++ b/academic/staden/staden.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for staden
 
-# Copyright 2011  Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2011-2012  Petar Petrov, ppetrov@paju.oulu.fi
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -24,7 +24,7 @@
 
 PRGNAM=staden		
 VERSION=${VERSION:-2.0.0b9}
-BUILD=${BUILD:-1}
+BUILD=${BUILD:-2}
 TAG=${TAG:-_SBo}	
 
 if [ -z "$ARCH" ]; then
@@ -37,7 +37,7 @@ fi
 
 SLKTCL=tcl8.5.9		# Slackware 13.37 sources for TCL
 SLKTK=tk8.5.9		# Slackware 13.37 sources for TK
-TKLIB=tklib0.5		# Folder name of TKLIB libraries, see line 117.
+TKLIB=tklib0.5		# Folder name of TKLIB
 
 CWD=$(pwd)
 TMP=${TMP:-/tmp/SBo}
@@ -95,6 +95,14 @@ sed -i "s:$STADENROOT/lib:$STADENROOT/lib${LIBDIRSUFFIX}:g" \
   prefinish/finish_sanger prefinish/prefinish pregap4/pregap4 spin/spin \
   spin_emboss/create_emboss_files trev/trev
 
+# Point to the right place of the EMBOSS .acd and data files. This is
+# needed if the "create_emboss_files" script is run after install.
+sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl
+sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin
+
+# Correct the path where staden components look for their manual.
+sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config
+
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -113,7 +121,7 @@ make install DESTDIR=$PKG
 # Build documentation. In the process, texi2dvi looks for tex and
 # that's why the SlackBuild should be run as real root (su -).
 # ## (or just source /etc/profile ) --rworkman
-cd ../${PRGNAM}_doc-$VERSION-src
+cd $TMP/$PRGNAM-$VERSION/${PRGNAM}_doc-$VERSION-src
 
 # Fix the doc and man pages paths
 sed "s:{datarootdir}/doc/staden:{prefix}/doc/$PRGNAM-$VERSION:" -i Makefile
@@ -130,6 +138,9 @@ make install DESTDIR=$PKG
 # Now that we're done building, let's remove those symlinks from earlier...
 rm -f /tmp/$SLKTCL /tmp/$SLKTK
 
+# This is empty
+rm -rf $PKG/usr/share/doc
+
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
@@ -137,17 +148,13 @@ find $PKG/usr/man -type f -exec gzip -9 {} \;
 for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
 
 mkdir -p $PKG/usr/share/{applications,pixmaps}
-cp $CWD/desktop/* $PKG/usr/share/applications
-cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
+cp $CWD/desktop/*.desktop $PKG/usr/share/applications
+cp $CWD/desktop/*.png $PKG/usr/share/pixmaps
 
-mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cd ../$PRGNAM-$VERSION-src
 cp -a ChangeLog NEWS README.build $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
-# Staden components expect the manual to be in /usr/share/doc/staden.
-ln -s $PRGNAM-$VERSION $PKG/usr/doc/$PRGNAM
-rm -rf $PKG/usr/share/doc # This is empty
 
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
diff --git a/academic/staden/staden.png b/academic/staden/staden.png
deleted file mode 100644
index d57d0e1bcb189..0000000000000
--- a/academic/staden/staden.png
+++ /dev/null