Browse Source

ap/primer3: Added.

slackware-14.2
Damien Goutte-Gattat 13 years ago
parent
commit
450a73d3af
  1. 1
      ap/primer3/primer3-1.1.4.tar.gz.sha1
  2. 105
      ap/primer3/primer3.SlackBuild
  3. 12
      ap/primer3/slack-desc

1
ap/primer3/primer3-1.1.4.tar.gz.sha1

@ -0,0 +1 @@
fcabf7d8aa31c5568bd130b318c3ead4a1b9aa3a primer3-1.1.4.tar.gz

105
ap/primer3/primer3.SlackBuild

@ -0,0 +1,105 @@
#!/bin/bash
# Build script for Slackware
# Damien Goutte-Gattat "gouttegd" < damien.goutte-gattat at e.ujf-grenoble.fr >
#
# Redistribution and use of this script, with or without modifications, 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.
#
# Latest primer3 sourcecode is available at:
# http://primer3.sourceforge.net/
# Source package infos
NAMESRC=${NAMESRC:-primer3}
VERSION=${VERSION:-1.1.4}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
WGET=${WGET:-http://switch.dl.sourceforge.net/sourceforge/primer3/$ARCHIVE}
# Built package infos
NAMETGZ=${NAMETGZ:-primer3}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-i486}
TARGET=${TARGET:-i486}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMETGZ}
CWD=$(pwd)
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exist or is not a directory!"
exit 1
fi
# Compilation flags
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
*)
CPUOPT="-O2"
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget "$WGET"
fi
sha1sum -c $ARCHIVE.sha1
# Compile
cd $TMP
echo "Building $ARCHIVE..."
mkdir $NAMETGZ-$VERSION && tar xf $CWD/$ARCHIVE -C $NAMETGZ-$VERSION
cd $NAMETGZ-$VERSION
make -j 2 -C src O_OPTS="$CPUOPT"
# Install
mkdir -p $PKG/usr/bin
install -s -m 755 src/primer3_core $PKG/usr/bin/primer3
install -s -m 755 src/{oligotm,ntdpal,long_seq_tm_test} $PKG/usr/bin
# Install the documentation
mkdir -p $PKG/usr/doc/$NAMETGZ-$VERSION
install -m 644 \
COPYING.txt README.txt how-to-cite.txt example src/release_notes.txt \
$PKG/usr/doc/$NAMETGZ-$VERSION
# Copy slack-desc file
install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMETGZ-$VERSION-$ARCH-$BUILD.tgz
rm -rf $PKG
rm -rf $TMP/$NAMETGZ-$VERSION
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

12
ap/primer3/slack-desc

@ -0,0 +1,12 @@
|-----handy-ruler------------------------------------------------------|
primer3: primer3 (PCR primer design tool)
primer3:
primer3: Primer3 picks primer for PCR reactions, considering various criteria
primer3: suchs as oligo melting temperature (TM), size, GC content, size of
primer3: PCR product, etc.
primer3:
primer3: S. Rozen and H. J. Skaletsky (2000). Primer3 on the WWW for general
primer3: users and for biologist programmers. In: Krawetz S, Misener S (eds).
primer3: Bioinformatics Methods and Protocols: Methods in Molecular Biology.
primer3: Humana Press, Totowa, NJ, pp 365-385.
primer3:
Loading…
Cancel
Save