academic/staden: Updated for version 2.0.0b10.

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

1 files changed, 19 insertions, 74 deletions

diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild
index cb3ee341df30e..3c132c0b6dd2b 100644
--- a/academic/staden/staden.SlackBuild
+++ b/academic/staden/staden.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for staden
 
-# Copyright 2011-2012  Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2011-2014  Petar Petrov, petar.petrov@student.oulu.fi
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,8 +23,8 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=staden
-VERSION=${VERSION:-2.0.0b9}
-BUILD=${BUILD:-3}
+VERSION=${VERSION:-2.0.0b10}
+BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
@@ -35,9 +35,7 @@ if [ -z "$ARCH" ]; then
   esac
 fi
 
-SLKTCL=tcl8.6.1		# Slackware 14.1 sources for TCL
-SLKTK=tk8.6.1		# Slackware 14.1 sources for TK
-TKLIB=tklib0.5		# Folder name of TKLIB
+TKLIB=tklib0.5	# Folder name of TKLIB
 
 CWD=$(pwd)
 TMP=${TMP:-/tmp/SBo}
@@ -63,51 +61,19 @@ set -e
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf $PRGNAM-$VERSION
-mkdir $PRGNAM-$VERSION
-cd $PRGNAM-$VERSION
+rm -rf $PRGNAM-$VERSION-src
 tar xvf $CWD/$PRGNAM-$VERSION-src.tar.gz
-tar xvf $CWD/${PRGNAM}_doc-$VERSION-src.tar.gz
-
-# The sources of TCL and TK are expected to be in /tmp at build time,
-# so we unpack them in the build directory and create symlinks in /tmp.
-rm -f /tmp/$SLKTCL
-rm -f /tmp/$SLKTK
-tar xvf $CWD/$SLKTCL-src.tar.xz
-tar xvf $CWD/$SLKTK-src.tar.xz
-ln -s $TMP/$PRGNAM-$VERSION/$SLKTCL /tmp/$SLKTCL
-ln -s $TMP/$PRGNAM-$VERSION/$SLKTK /tmp/$SLKTK
-
-chown -R root:root $PRGNAM-$VERSION-src  ${PRGNAM}_doc-$VERSION-src
-find $PRGNAM-$VERSION-src  ${PRGNAM}_doc-$VERSION-src \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
-
 cd $PRGNAM-$VERSION-src
-
-# On Slackware64, the components of staden (like GAP4, GAP5, PREGAP4,
-# SPIN, TREV) will not run, as they still expect their libraries to be
-# in /usr/lib not /usr/lib64. Let's correct the libraries path.
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# Make sure libraries path is correct.
 sed -i "s:$STADENROOT/lib:$STADENROOT/lib${LIBDIRSUFFIX}:g" \
-  global.mk staden.profile copy_reads/copy_reads gap4/gap4 gap5/gap5 \
-  gap5/gap5_consensus gap5/gap5_export gap5/tg_index gap5/tg_view \
-  prefinish/finish_sanger prefinish/prefinish pregap4/pregap4 spin/spin \
-  spin_emboss/create_emboss_files trev/trev
-
-# Point to the right place of the EMBOSS .acd and data files. This is
-# needed if the "create_emboss_files" script is run after install.
-sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl
-sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin
-
-# Correct the path where staden components look for their manual.
-sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config
-
-# These fixes are from Arch linux AUR
-# http://aur.archlinux.org/packages/st/staden/PKGBUILD
-sed -i 's:-DSVN_VERSION=$(SVNVERS)::' system.mk.in
-sed -i "s/gzFile\ \*gz/gzFile\ gz/" gap5/zfio.h
+  global.mk staden.profile
 
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
@@ -124,41 +90,20 @@ CXXFLAGS="$SLKCFLAGS" \
 make
 make install DESTDIR=$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 $TMP/$PRGNAM-$VERSION/${PRGNAM}_doc-$VERSION-src
-
-# Fix the doc and man pages paths
-sed "s:{datarootdir}/doc/staden:{prefix}/doc/$PRGNAM-$VERSION:" -i Makefile
-sed "s:{datarootdir}/man:{prefix}/man:" -i Makefile
-
-# Remove this, or there will be an error at the "make install" line.
-rm -rf i/i
-
-# Generate documentation. If you want it in the US letter format,
-# change the next line to "make unix PAPER=us".
-make unix
-make install DESTDIR=$PKG
-
-# Now that we're done building, let's remove those symlinks from earlier...
-rm -f /tmp/$SLKTCL /tmp/$SLKTK
-
-# This is empty
+# These are empty
 rm -rf $PKG/usr/share/doc
+rm -rf $PKG/usr/man
 
 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
 
-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/*.desktop $PKG/usr/share/applications
 cp $CWD/desktop/*.png $PKG/usr/share/pixmaps
 
-cd ../$PRGNAM-$VERSION-src
-cp -a ChangeLog NEWS README.build $PKG/usr/doc/$PRGNAM-$VERSION
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a ChangeLog LICENCE.txt 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