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@ -1,6 +1,6 @@
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#!/bin/bash
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# Build script for Slackware
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# Copyright (C) 2014 Damien Goutte-Gattat
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# Copyright (C) 2014,2016 Damien Goutte-Gattat
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#
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# Redistribution and use of this script, with or without modifications,
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# is permitted provided that the following conditions are met:
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@ -27,13 +27,13 @@
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# Source package infos
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NAMESRC=${NAMESRC:-RNAstructure}
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VERSION=${VERSION:-5.6}
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VERSION=${VERSION:-5.8.1}
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ARCHIVE=${ARCHIVE:-${NAMESRC}Source.tgz}
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WGET=${WGET:-http://rna.urmc.rochester.edu/$ARCHIVE}
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# Build infos
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NAMEPKG=${NAMEPKG:-RNAstructure}
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BUILD=${BUILD:-2GGD}
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BUILD=${BUILD:-1GGD}
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ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
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JOBS=${JOBS:-1}
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EXT=${EXT:-txz}
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@ -57,7 +57,11 @@ if [ ! -d $TMP ]; then
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fi
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LIBDIRSUFFIX=""
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[ "x$ARCH" = xx86_64 ] && LIBDIRSUFFIX="64"
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LIBNAMESUFFIX=""
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if [ "x$ARCH" = xx86_64 ] ; then
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LIBDIRSUFFIX="64"
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LIBNAMESUFFIX="_64"
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fi
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# Get and verify the source archive
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if [ ! -r $ARCHIVE ]; then
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@ -72,16 +76,14 @@ cd $TMP
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echo "Building $ARCHIVE..."
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tar xf $CWD/$ARCHIVE
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cd $NAME
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sed -i "s,^INCLUDEPATH1 =.*$,INCLUDEPATH1 = \"/usr/lib$LIBDIRSUFFIX/jdk1.7.0_45/include\"," compiler.h
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sed -i "s,^INCLUDEPATH2 =.*$,INCLUDEPATH2 = \"/usr/lib$LIBDIRSUFFIX/jdk1.7.0_45/include/linux\"," compiler.h
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make all
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(cd RNAstructure_java_interface
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make GUI
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(cd java_interface
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make gui
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)
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# Install binaries
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mkdir -p $PKG/usr/libexec/RNAstructure $PKG/usr/lib$LIBDIRSUFFIX $PKG/usr/share/RNAstructure
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for exe in AllSub CircleCompare DuplexFold DynalignDotPlot EnergyPlot Fold MaxExpect NAPSS ProbKnot ProbabilityPlot ProbablePair RemovePseudoknots ShapeKnots TurboFold bifold bipartition ct2dot dot2ct draw dynalign efn2 multilign oligoscreen partition refold scorer stochastic ; do
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for exe in AccessFold AllSub CircleCompare DuplexFold DynalignDotPlot EnergyPlot EnsembleEnergy Fold Fold-smp MaxExpect NAPSS OligoWalk PARTS ProbKnot ProbabilityPlot ProbablePair RemovePseudoknots ShapeKnots TurboFold TurboFold-smp bifold bipartition ct2dot design dot2ct draw dynalign dynalign_ii efn2 multilign oligoscreen partition phmm refold scorer stochastic ; do
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if [ -f exe/$exe-smp ]; then
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install -m 755 -s exe/$exe-smp $PKG/usr/libexec/RNAstructure/$(echo $exe | tr [A-Z] [a-z])
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else
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@ -93,7 +95,9 @@ done
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install -m 755 -D $CWD/rna.sh $PKG/usr/bin/rna
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# Install Java program
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install -m 755 -s exe/libRNAstructure_GUI.so $PKG/usr/lib$LIBDIRSUFFIX
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install -m 755 -s exe/libRNAstructure_GUI$LIBNAMESUFFIX.so \
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$PKG/usr/lib$LIBDIRSUFFIX
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install -m 644 exe/RNAstructure.jar $PKG/usr/share/RNAstructure
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cat > $PKG/usr/bin/RNAstructure <<EOF
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#!/bin/sh
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