academic/primer3: Updated for version 2.3.4.

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

1 files changed, 35 insertions, 12 deletions

diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild
index 150008b4f319..09cf5104ce09 100644
--- a/academic/primer3/primer3.SlackBuild
+++ b/academic/primer3/primer3.SlackBuild
@@ -1,18 +1,30 @@
 #!/bin/sh
 
 # Slackware build script for primer3
-# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
-# hereby submitted to the public domain
 
-# Thanks to Niels Horn for correcting the CFLAGS.
-
-# 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 2011-2012  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=primer3
-VERSION=${VERSION:-2.2.3}
-BUILD=${BUILD:-2}
+VERSION=${VERSION:-2.3.4}
+BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
@@ -62,6 +74,9 @@ cd ./src
 #Use our CFLAGS
 sed -i "/^CFLAGS/s/=/+=/" Makefile
 
+# Look for configuration files in /usr/share instead of /opt
+sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c
+
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 make
@@ -71,14 +86,22 @@ make
 # make test
 
 install -D -m755 primer3_core $PKG/usr/bin/primer3_core
-install -D -m755 long_seq_tm_test $PKG/usr/bin/long_seq_tm_test
 install -D -m755 ntdpal $PKG/usr/bin/ntdpal
 install -D -m755 ntthal $PKG/usr/bin/ntthal
 install -D -m755 oligotm $PKG/usr/bin/oligotm
 
-# eprimer32 from EMBOSS expects the binary to be called primer32_core
-ln -s primer3_core $PKG/usr/bin/primer32_core
+# eprimer32 from EMBOSS, expects the binary to be called primer32_core
+cd $PKG/usr/bin
+ln -s primer3_core primer32_core
+
+# Copy configuration files and settings to /usr/share
 cd $TMP/$PRGNAM-$VERSION
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a src/primer3_config \
+  primer3_v1_1_4_default_settings.txt \
+  primer3web_v0_4_0_default_settings.txt \
+  primer3web_v3_0_0_default_settings.txt \
+  $PKG/usr/share/$PRGNAM
 
 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