Browse Source

ap/RNAstructure: Removed.

current-20191101
Damien Goutte-Gattat 2 years ago
parent
commit
edbf2d3160
  1. 134
      ap/RNAstructure/RNAstructure.SlackBuild
  2. 1
      ap/RNAstructure/RNAstructureSource.tgz.sha1
  3. 21
      ap/RNAstructure/rna.sh
  4. 12
      ap/RNAstructure/slack-desc

134
ap/RNAstructure/RNAstructure.SlackBuild

@ -1,134 +0,0 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2014,2016 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:-5.8.1}
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=""
LIBNAMESUFFIX=""
if [ "x$ARCH" = xx86_64 ] ; then
LIBDIRSUFFIX="64"
LIBNAMESUFFIX="_64"
fi
# 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
make all
(cd java_interface
make gui
)
# Install binaries
mkdir -p $PKG/usr/libexec/RNAstructure $PKG/usr/lib$LIBDIRSUFFIX $PKG/usr/share/RNAstructure
for exe in AccessFold AllSub CircleCompare DuplexFold DynalignDotPlot EnergyPlot EnsembleEnergy Fold Fold-smp MaxExpect NAPSS OligoWalk PARTS ProbKnot ProbabilityPlot ProbablePair RemovePseudoknots ShapeKnots TurboFold TurboFold-smp bifold bipartition ct2dot design dot2ct draw dynalign dynalign_ii efn2 multilign oligoscreen partition phmm refold scorer stochastic ; do
if [ -f exe/$exe-smp ]; then
install -m 755 -s exe/$exe-smp $PKG/usr/libexec/RNAstructure/$(echo $exe | tr [A-Z] [a-z])
else
install -m 755 -s exe/$exe $PKG/usr/libexec/RNAstructure/$(echo $exe | tr [A-Z] [a-z])
fi
done
# Install launcher script
install -m 755 -D $CWD/rna.sh $PKG/usr/bin/rna
# Install Java program
install -m 755 -s exe/libRNAstructure_GUI$LIBNAMESUFFIX.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

1
ap/RNAstructure/RNAstructureSource.tgz.sha1

@ -1 +0,0 @@
bf5d33d0904a0c8f86bbbe84aae3bf21979e73e2 RNAstructureSource.tgz

21
ap/RNAstructure/rna.sh

@ -1,21 +0,0 @@
#!/bin/sh
export DATAPATH=/usr/share/RNAstructure/data_tables
program=$1
if [ -z "$program" ]; then
echo "rna: command expected" >&2
echo "Available commands:" >&2
ls /usr/libexec/RNAstructure >&2
exit 1
elif [ ! -x /usr/libexec/RNAstructure/$program ]; then
echo "rna: command not found" >&2
echo "Available commands:" >&2
ls /usr/libexec/RNAstructure >&2
exit 2
fi
shift
exec /usr/libexec/RNAstructure/$program "$@"

12
ap/RNAstructure/slack-desc

@ -1,12 +0,0 @@
|-----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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