academic/staden: A few enhancements.

Signed-off-by: bedlam <dave@slackbuilds.org>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 80 insertions, 16 deletions

diff --git a/academic/staden/README b/academic/staden/README
index 0d8a67c590..aa36fdbcd8 100644
--- a/academic/staden/README
+++ b/academic/staden/README
@@ -1,20 +1,40 @@
 The programs part of the Staden package provide an excellent and 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 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.
+
+NOTE: Xfce submenus
+For XFCE, if you want to have the menu entries grouped in a submenu
+folder (multilevel menu entry), do:
+
+  SUBMENU="YES" ./staden.SlackBuild
+
+NOTE: Staden and EMBOSS:
+Staden used to provide a GUI for (at least part of) the programs from
+EMBOSS. To give it a try, run this after install (of course you need to
+have installed EMBOSS, too):
+
+  create_emboss_files
+
+This will create some files in:
+
+  /usr/share/staden/tcl/spin_emboss/acdtcl/
+
+CITING
 For more information and citing, visit Staden's web page and check the
 "References" file in the documentation.
diff --git a/academic/staden/desktop/staden.directory b/academic/staden/desktop/staden.directory
new file mode 100644
index 0000000000..2623e56005
--- /dev/null
+++ b/academic/staden/desktop/staden.directory
@@ -0,0 +1,4 @@
+[Desktop Entry]
+Type=Directory
+Name=Staden Package
+Icon=folder
diff --git a/academic/staden/desktop/staden.menu b/academic/staden/desktop/staden.menu
new file mode 100644
index 0000000000..3f5ba10187
--- /dev/null
+++ b/academic/staden/desktop/staden.menu
@@ -0,0 +1,20 @@
+<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN"
+"http://www.freedesktop.org/standards/menu-spec/menu-1.0.dtd">
+<Menu>
+  <Name>Applications</Name>
+  <Menu>
+    <Name>Education</Name>
+    <Directory>xfce4-education.directory</Directory>
+  <Menu>
+    <Name>Staden Package</Name>
+    <Directory>staden.directory</Directory>
+    <Include>
+	<Filename>gap4.desktop</Filename>
+	<Filename>gap5.desktop</Filename>
+	<Filename>pregap4.desktop</Filename>      
+	<Filename>trev.desktop</Filename>
+      	<Filename>spin.desktop</Filename>
+    </Include>
+  </Menu>
+  </Menu>
+</Menu>
diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild
index 2c2bea2c39..4c16f47019 100644
--- a/academic/staden/staden.SlackBuild
+++ b/academic/staden/staden.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for staden
 
-# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=staden
 VERSION=${VERSION:-2.0.0b11}
-BUILD=${BUILD:-1}
+BUILD=${BUILD:-2}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
 
@@ -97,6 +97,11 @@ CXXFLAGS="$SLKCFLAGS" \
   --with-tklib=/usr/lib${LIBDIRSUFFIX}/$TKLIB \
   --build=$ARCH-slackware-linux
 
+# 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
+
 make
 make install DESTDIR=$PKG
 
@@ -111,6 +116,21 @@ mkdir -p $PKG/usr/share/{applications,pixmaps}
 cp $CWD/desktop/*.desktop $PKG/usr/share/applications
 cp $CWD/desktop/*.png $PKG/usr/share/pixmaps
 
+# Do we want a submenu? For more info:
+# https://slackalaxy.com/2021/08/08/xfce-multilevel-menu/
+if [ $SUBMENU = "YES" ]; then
+  # Use a separate "Staden Package" menu entry within "Education"	
+  mkdir -p $PKG/etc/xdg/menus/applications-merged
+  cp $CWD/desktop/$PRGNAM.menu $PKG/etc/xdg/menus/applications-merged
+  
+  # Menu directory structure
+  mkdir -p $PKG/usr/share/desktop-directories
+  cp $CWD/desktop/$PRGNAM.directory $PKG/usr/share/desktop-directories
+
+  # The category in the .desktop files is commented out to avoid duplication in menus
+  sed -i "s:Categories:#Categories:" $PKG/usr/share/applications/*.desktop
+fi
+
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a ChangeLog LICENCE.txt NEWS README.build \
   $PKG/usr/doc/$PRGNAM-$VERSION