academic/genpak: Various packaging fixes

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

academic/genpak/README

@@ -6,5 +6,4 @@ determine codon usage / GC contents, do promotor searches, calculate
 Tm, search for restriction sites, convert sequences into numerical 
 representations and much more.
 
-You most likely want to install arka, which provides a GUI for GenPak. 
-Arka is also available at SlackBuilds.org.
+You most likely want to install Arka, which provides a GUI for GenPak.

academic/genpak/genpak.SlackBuild

@@ -1,16 +1,30 @@
 #!/bin/sh
 
 # Slackware build script for genpak
-# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
-# hereby submitted to the public domain
 
-# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
-# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
-# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+# Copyright 2011  Petar Petrov, ppetrov@paju.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=genpak			
 VERSION=${VERSION:-0.26}	
-BUILD=${BUILD:-3}
+BUILD=${BUILD:-4}
 TAG=${TAG:-_SBo}		
 
 if [ -z "$ARCH" ]; then
@@ -55,57 +69,25 @@ find . \
  \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
  -exec chmod 644 {} \;
 
-# Use our CFLAGS
-sed -i "/^CFLAGS/s/=/+=/" Makefile
+# arch-independent data files belong in /usr/share:
+sed -i "s,usr/lib/,usr/share/,g" src/* man1/* html/* *.TXT
 
-# Correct libdir
-sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" Makefile
-sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" src/genpak.c
-sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" src/genpak.h
+make \
+  CFLAGS="$SLKCFLAGS" \
+  TREE=/usr \
+  BINDIR=/usr/bin \
+  DATADIR=/usr/share \
+  MANDIR=/usr/man \
+  DOCDIR=/usr/doc
 
-CFLAGS="$SLKCFLAGS" \
-CXXFLAGS="$SLKCFLAGS" \
-  make
+mkdir -p $PKG/usr/{bin,doc,man/man1,share}
 
-# Makefile does not support "make DESTDIR install". So...
-cd ./src
-install -D -m755 gp_acc		$PKG/usr/bin/gp_acc
-install -D -m755 gp_adjust	$PKG/usr/bin/gp_adjust
-install -D -m755 gp_cdndev	$PKG/usr/bin/gp_cdndev
-install -D -m755 gp_cusage	$PKG/usr/bin/gp_cusage
-install -D -m755 gp_digest	$PKG/usr/bin/gp_digest
-install -D -m755 gp_dimer	$PKG/usr/bin/gp_dimer
-install -D -m755 gp_findorf	$PKG/usr/bin/gp_findorf
-install -D -m755 gp_gc		$PKG/usr/bin/gp_gc
-install -D -m755 gp_getseq	$PKG/usr/bin/gp_getseq
-install -D -m755 gp_matrix	$PKG/usr/bin/gp_matrix
-install -D -m755 gp_mkmtx	$PKG/usr/bin/gp_mkmtx
-install -D -m755 gp_pars	$PKG/usr/bin/gp_pars
-install -D -m755 gp_pattern	$PKG/usr/bin/gp_pattern
-install -D -m755 gp_primer	$PKG/usr/bin/gp_primer
-install -D -m755 gp_qs		$PKG/usr/bin/gp_qs
-install -D -m755 gp_randseq	$PKG/usr/bin/gp_randseq
-install -D -m755 gp_scan	$PKG/usr/bin/gp_scan
-install -D -m755 gp_seq2prot	$PKG/usr/bin/gp_seq2prot
-install -D -m755 gp_shift	$PKG/usr/bin/gp_shift
-install -D -m755 gp_slen	$PKG/usr/bin/gp_slen
-install -D -m755 gp_tm		$PKG/usr/bin/gp_tm
-install -D -m755 gp_trimer	$PKG/usr/bin/gp_trimer
-
-cd ../data
-install -D -m644 ecoli.mtx	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/ecoli.mtx
-install -D -m644 enzyme.enz	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/enzyme.enz
-install -D -m644 myco.cdn	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco.cdn
-install -D -m644 myco.mtx	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco.mtx
-install -D -m644 myco0		$PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco0
-install -D -m644 sample.seq	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/sample.seq
-install -D -m644 standard.cdn	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/standard.cdn
-install -D -m644 mporfs.seq	$PKG/usr/lib${LIBDIRSUFFIX}/genpak/mporfs.seq
-
-# Put man pages to their proper place
-mkdir -p $PKG/usr/man/man1
-cp ../man1/* $PKG/usr/man/man1
-cd ..
+make install docs \
+  TREE=$PKG/usr \
+  BINDIR=$PKG/usr/bin \
+  DATADIR=$PKG/usr/share \
+  MANDIR=$PKG/usr/man \
+  DOCDIR=$PKG/usr/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
@@ -113,10 +95,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 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 $PKG/usr/doc/$PRGNAM-$VERSION
-cp -a \
-  html CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT \
-  $PKG/usr/doc/$PRGNAM-$VERSION/
+( cd $PKG/usr/doc ; mv gp $PRGNAM-$VERSION ; ln -s $PRGNAM-$VERSION gp )
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 
 mkdir -p $PKG/install

academic/genpak/genpak.info

@@ -7,4 +7,4 @@ DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 MAINTAINER="Petar Petrov"
 EMAIL="ppetrov@paju.oulu.fi"
-APPROVED="Erik Hanson,Niels Horn"
+APPROVED="rworkman"

academic/genpak/slack-desc

@@ -12,8 +12,8 @@ genpak: Genpak is a set of small utilities written in ANSI C to manipulate
 genpak: DNA sequences in a Unix fashion, fit for combining within shell
 genpak: and cgi scripts.
 genpak:
-genpak:
-genpak:
-genpak:
-genpak:
 genpak: Home: http://www.bioinformatics.org/genpak/
+genpak:
+genpak:
+genpak:
+genpak: