ap/RNAstructure: Added RNAstructure-5.6.

slackware-14.2
Damien Goutte-Gattat 9 years ago
parent da7bf90420
commit c9a0e97578
  1. 127
      ap/RNAstructure/RNAstructure.SlackBuild
  2. 1
      ap/RNAstructure/RNAstructureSource.tgz.sha1
  3. 12
      ap/RNAstructure/slack-desc

@ -0,0 +1,127 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2014 Damien Goutte-Gattat
#
# 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.
#
# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
#
# Latest RNAstructure sourcecode is available at:
# <http://rna.urmc.rochester.edu/RNAstructureDownload.html>.
# Source package infos
NAMESRC=${NAMESRC:-RNAstructure}
VERSION=${VERSION:-5.6}
ARCHIVE=${ARCHIVE:-${NAMESRC}Source.tgz}
WGET=${WGET:-http://rna.urmc.rochester.edu/$ARCHIVE}
# Build infos
NAMEPKG=${NAMEPKG:-RNAstructure}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
JOBS=${JOBS:-1}
EXT=${EXT:-txz}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(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 exists or is not a directory!"
exit 1
fi
LIBDIRSUFFIX=""
[ "x$ARCH" = xx86_64 ] && LIBDIRSUFFIX="64"
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget -c -O $ARCHIVE.part "$WGET"
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Compile
cd $TMP
echo "Building $ARCHIVE..."
tar xf $CWD/$ARCHIVE
cd $NAME
sed -i "s,^INCLUDEPATH1 =.*$,INCLUDEPATH1 = \"/usr/lib$LIBDIRSUFFIX/jdk1.7.0_45/include\"," compiler.h
sed -i "s,^INCLUDEPATH2 =.*$,INCLUDEPATH2 = \"/usr/lib$LIBDIRSUFFIX/jdk1.7.0_45/include/linux\"," compiler.h
make all
(cd RNAstructure_java_interface
make GUI
)
# Install binaries
mkdir -p $PKG/usr/bin $PKG/usr/lib$LIBDIRSUFFIX $PKG/usr/share/RNAstructure
for exe in bifold bipartition ct2dot dot2ct draw dynalign efn2 multilign oligoscreen partition refold scorer stochastic ; do
if [ -f exe/$exe-smp ]; then
install -m 755 -s exe/$exe-smp $PKG/usr/bin/$exe
else
install -m 755 -s exe/$exe $PKG/usr/bin/$exe
fi
done
# Install Java program
install -m 755 -s exe/libRNAstructure_GUI.so $PKG/usr/lib$LIBDIRSUFFIX
install -m 644 exe/RNAstructure.jar $PKG/usr/share/RNAstructure
cat > $PKG/usr/bin/RNAstructure <<EOF
#!/bin/sh
export DATAPATH=/usr/share/RNAstructure/data_tables
exec java -jar /usr/share/RNAstructure/RNAstructure.jar
EOF
chmod 755 $PKG/usr/bin/RNAstructure
# Install data
cp -r data_tables $PKG/usr/share/RNAstructure
# Install the documentation
mkdir -p $PKG/usr/doc/$NAMEPKG-$VERSION
install -m 644 ReadMe.txt gpl.txt $PKG/usr/doc/$NAMEPKG-$VERSION
cp -r manual $PKG/usr/doc/$NAMEPKG-$VERSION
cp -r examples $PKG/usr/doc/$NAMEPKG-$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 $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

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bb87a56f87a34b440c826fd9864230ebc9eaa704 RNAstructureSource.tgz

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|-----handy-ruler-----------------------------------------------------|
RNAstructure: RNAstructure (RNA secondary structure analysis tools)
RNAstructure:
RNAstructure: This package provides RNAstructure, which includes tools for RNA
RNAstructure: secondary structure prediction and analysis.
RNAstructure:
RNAstructure:
RNAstructure:
RNAstructure:
RNAstructure:
RNAstructure:
RNAstructure:
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