academic/primer3: Updated for version 2.3.4.

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

5 files changed, 49 insertions, 25 deletions

diff --git a/academic/primer3/README b/academic/primer3/README
index 2ef54f3a5a..51977f2f12 100644
--- a/academic/primer3/README
+++ b/academic/primer3/README
@@ -1,11 +1,14 @@
-Primer3 is a widely used program for designing PCR primers. Primer3 
-can also design hybridization probes and sequencing primers. PCR is 
-used for many different goals. Consequently, primer3 has many 
-different input parameters that you control and that tell primer3 
+Primer3 is a widely used program for designing PCR primers (PCR =
+"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
+in genetics and molecular biology. Primer3 can design hybridization
+probes and sequencing primers.
+
+PCR is used for many different goals. Consequently, primer3 has many
+different input parameters that you control and that tell primer3
 exactly what characteristics make good primers for your goals.
 
 For details and citation:
-Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for 
-general users and for biologist programmers. In: Krawetz S, Misener S 
-(eds) Bioinformatics Methods and Protocols: Methods in Molecular 
+Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
+general users and for biologist programmers. In: Krawetz S, Misener S
+(eds) Bioinformatics Methods and Protocols: Methods in Molecular
 Biology. Humana Press, Totowa, NJ, pp 365-386
diff --git a/academic/primer3/References b/academic/primer3/References
index 7f4646bd80..5009a52a1b 100644
--- a/academic/primer3/References
+++ b/academic/primer3/References
@@ -1,5 +1,3 @@
-References
-
 Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general
 users and for biologist programmers. In: Krawetz S, Misener S (eds)
 Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana
diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild
index 150008b4f3..09cf5104ce 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
diff --git a/academic/primer3/primer3.info b/academic/primer3/primer3.info
index 3ebd4bbaa2..9c5bb8fbb9 100644
--- a/academic/primer3/primer3.info
+++ b/academic/primer3/primer3.info
@@ -1,8 +1,8 @@
 PRGNAM="primer3"
-VERSION="2.2.3"
+VERSION="2.3.4"
 HOMEPAGE="http://primer3.sourceforge.net/"
-DOWNLOAD="http://downloads.sourceforge.net/project/primer3/primer3/2.2.3/primer3-2.2.3.tar.gz"
-MD5SUM="b9cdcff68637479c094844d652c03839"
+DOWNLOAD="http://downloads.sourceforge.net/project/primer3/primer3/2.3.4/primer3-2.3.4.tar.gz"
+MD5SUM="06029a16dccf1bcec70fd427d3c44850"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
diff --git a/academic/primer3/slack-desc b/academic/primer3/slack-desc
index 7956929b4b..dae2bbb6a5 100644
--- a/academic/primer3/slack-desc
+++ b/academic/primer3/slack-desc
@@ -13,7 +13,7 @@ primer3: "Polymerase Chain Reaction"). PCR is an essential and
 primer3: ubiquitous tool in genetics and molecular biology. Primer3 can also
 primer3: design hybridization probes and sequencing primers.
 primer3:
+primer3: Home: http://primer3.sourceforge.net/
 primer3:
 primer3:
 primer3:
-primer3: Home: http://primer3.sourceforge.net/