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#!/bin/bash |
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# Build script for Slackware |
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# Damien Goutte-Gattat "gouttegd" <damien.goutte-gattat at e.ujf-grenoble.fr> |
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# |
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# Redistribution and use of this script, with or without modifications, is |
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# permitted provided that the following conditions are met: |
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# |
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# 1. Redistributions of this script must retain the above copyright |
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# notice, this list of conditions and the following disclaimer. |
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# |
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR IMPLIED |
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF |
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO |
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, |
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, |
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; |
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, |
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR |
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF |
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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# |
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# Latest ncbi sourcecode is available at: |
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# ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT |
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# |
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# The build process used in this slackbuild is based on the Debian |
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# NCBI-related packages, maintained by Aaron M. Ucko <ucko@debian.org>. |
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# Source package infos |
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NAMESRC=${NAMESRC:-ncbi} |
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VERSION=${VERSION:-6.1} |
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ARCHIVE=${ARCHIVE:-$NAMESRC.tar.gz} |
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WGET=${WGET:-ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20070822/$ARCHIVE} |
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DEBPATCH=ncbi-tools6_6.1.20070822-1.diff.gz |
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DEBPATCH_URL=http://ftp.de.debian.org/debian/pool/main/n/ncbi-tools6/$DEBPATCH |
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# Built package infos |
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NAMETGZ=${NAMETGZ:-ncbi-toolkit} |
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BUILD=${BUILD:-1GGD} |
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ARCH=${ARCH:-i486} |
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TARGET=${TARGET:-i486} |
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# Directories |
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TMP=${TMP:-/tmp} |
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OUT=${OUT:-$TMP/build} |
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PKG=${PKG:-$OUT/$NAMETGZ} |
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CWD=$(pwd) |
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set -e # Quit if a command returns non-zero |
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# Sanity checks |
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if [ $UID -eq 0 ]; then |
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echo "You should NOT run this script as ROOT!" |
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exit 1 |
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fi |
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if [ ! -d $TMP ]; then |
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echo "$TMP does not exist or is not a directory!" |
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exit 1 |
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fi |
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# Compilation flags |
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case "$ARCH" in |
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i?86) |
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CPUOPT="-O2 -march=$ARCH -mtune=i686" |
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;; |
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*) |
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CPUOPT="-O2" |
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;; |
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esac |
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# Get and verify the source archive |
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if [ ! -r $ARCHIVE ]; then |
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wget "$WGET" |
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fi |
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if [ ! -r $DEBPATCH ]; then |
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wget "$DEBPATCH_URL" |
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fi |
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sha1sum -c $ARCHIVE.sha1 |
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sha1sum -c $DEBPATCH.sha1 |
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NAME=$(tar ft $ARCHIVE | head -1 | cut -d / -f 1) |
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# Extract archive and apply the Debian patch |
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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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zcat $CWD/$DEBPATCH | patch -p1 |
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# Compile |
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export NCBI_VERSION=$VERSION |
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export NCBI_VERSION_MAJOR=$(echo $VERSION | cut -d. -f1) |
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export NCBI_VERSION_MINOR=$(echo $VERSION | cut -d. -f2) |
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export BLAST_VERSION=$(cat demo/.BLAST_VERSION) |
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export NCBI_LBSM_SRC=ncbi_lbsmd_stub.c |
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export NCBI_LBSM_OBJ=ncbi_lbsmd_stub.o |
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export LD_LIBRARY_PATH=$TMP/$NAME/shlib:$LD_LIBRARY_PATH |
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cd build |
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ln -s ../make/*.unx . |
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ln -s ../make/ln-if-absent . |
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mv makeall.unx makefile |
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pmake all LCL=lnx CC=gcc RAN=ranlib \ |
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OTHERLIBS=-lm VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG=-DWIN_MOTIF \ |
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NCBI_LINKINGLIBDIR="../shlib -L../lib" \ |
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CFLAGS1="-c $CPUOPT -D_PNG -fPIC" \ |
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LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \ |
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LIB30=libncbicn3d.a LIB45=libddvlib.a \ |
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LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a |
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pmake -f makenet.unx LCL=lnx CC=gcc RAN=ranlib \ |
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OTHERLIBS=-lm VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG=-DWIN_MOTIF \ |
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NCBI_LINKINGLIBDIR="../shlib -L../lib" \ |
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CFLAGS1="-c $CPUOPT -fPIC" \ |
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NETENTREZVERSION=2.02c2ASN1SPEC6 \ |
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BLIB31=libvibnet.a OGLLIBS="-lGLU -lGL -lpng" \ |
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all libncbimla.a libnetblast.a libncbitxc2.a libncbiid1.a shlib |
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pmake clean |
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pmake all LCL=lnx CC=gcc RAN=ranlib \ |
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OTHERLIBS=-lm VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG=-DWIN_MOTIF \ |
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NCBI_LINKINGLIBDIR="../shlib -L../lib" \ |
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CFLAGS1="-c $CPUOPT -D_PNG" \ |
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LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \ |
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LIB30=libncbicn3d.a LIB45=libddvlib.a \ |
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LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a |
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pmake -f makedemo.unx LCL=lnx CC=gcc RAN=ranlib \ |
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OTHERLIBS=-lm VIBLIBS= VIBFLAG= \ |
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NCBI_LINKINGLIBDIR="../shlib -L../lib" \ |
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CFLAGS1="-c $CPUOPT" \ |
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LIB50=-lpcre |
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rm -f blast blastall blastall_old blastpgp seedtop megablast rpsblast \ |
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blastclust |
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pmake -f makedemo.unx LCL=lnx CC=gcc RAN=ranlib \ |
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OTHERLIBS=-lm THREAD_OBJ=ncbithr.o THREAD_OTHERLIBS=-lpthread \ |
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NCBI_LINKINGLIBDIR="../shlib -L../lib" \ |
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VIBLIBS= VIBFLAG= \ |
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blast blastall blastall_old blastpgp seedtop megablast rpsblast \ |
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blastclust |
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pmake -f makenet.unx LCL=lnx CC=gcc RAN=ranlib \ |
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OTHERLIBS=-lm VIBFLAG=-DWIN_MOTIF \ |
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NCBI_LINKINGLIBDIR="../shlib -L../lib" \ |
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CFLAGS1="-c $CPUOPT" \ |
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THREAD_OBJ=ncbithr.o THREAD_OTHERLIBS=-lpthread \ |
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NETENTREZVERSION=2.02c2ASN1SPEC6 \ |
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BLIB31=libvibnet.a OGLLIBS= VIBLIBS= \ |
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VIB="Psequin sbtedit udv ddv blastcl3 idfetch bl2seq asn2gb tbl2asn \ |
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gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml cleanasn \ |
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insdseqget nps2gps spidey trna2sap trna2tbl Cn3D" |
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# Prepare the package tree |
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cd $TMP/$NAME |
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mkdir -p $PKG/usr/lib |
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install -m 644 lib/* shlib/*.so.$VERSION $PKG/usr/lib |
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for x in ncbiacc ncbiCacc netentr; do |
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rm -f $PKG/usr/lib/lib$x.so.$VERSION |
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ln -s libncbiNacc.so.$NCBI_VERSION_MAJOR \ |
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$PKG/usr/lib/lib$x.so.$NCBI_VERSION_MAJOR |
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ln -s libncbiNacc.so $PKG/usr/lib/lib$x.so |
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done |
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for x in ncbicn3d vibrant; do |
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rm -f $PKG/usr/lib/lib$x.so.$VERSION |
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ln -s lib${x}OGL.so.$NCBI_VERSION_MAJOR \ |
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$PKG/usr/lib/lib$x.so.$NCBI_VERSION_MAJOR |
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ln -s lib${x}OGL.so $PKG/usr/lib/lib$x.so |
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done |
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cd $PKG/usr/lib |
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for f in *.so.$VERSION; do |
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base=$(basename $f .so.$VERSION) |
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ln -s $f $base.so.$NCBI_VERSION_MAJOR |
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ln -s $f $base.so |
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done |
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cd $TMP/$NAME |
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mkdir -p $PKG/usr/include/ncbi |
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cp -LRp include/* $PKG/usr/include/ncbi |
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cd $PKG/usr/include/ncbi |
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rm -f FSpCompat.h FullPath.h More*.h Optimization*.h pcre*.h |
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find . -type f | xargs chmod 644 |
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cd $TMP/$NAME |
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mkdir -p $PKG/usr/bin |
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install $(find build -type f -perm +111 -print) $PKG/usr/bin |
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install -m 755 debian/vibrate $PKG/usr/bin |
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rm -f $PKG/usr/bin/{dosimple,ncbisort,cdscan,entrcmd,*test*,*demo*} |
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mv $PKG/usr/bin/Cn3D $PKG/usr/bin/Cn3D-3.0 |
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mv $PKG/usr/bin/blast $PKG/usr/bin/blast2 |
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# Strip binaries |
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find $PKG | xargs file | grep "ELF 32-bit LSB" | cut -d : -f 1 | \ |
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xargs strip --strip-unneeded 2> /dev/null |
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# Install and compress man pages |
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mkdir -p $PKG/usr/man/man1 |
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install -m 644 doc/man/* $PKG/usr/man/man1 |
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install -m 644 debian/man/* $PKG/usr/man/man1 |
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rm -f $PKG/usr/man/man1/entrcmd.1 |
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find $PKG/usr/man/man1 -type f | xargs gzip -9 2> /dev/null |
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# Install the NCBI data |
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mkdir -p $PKG/usr/share/ncbi/data |
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install -m 644 data/* $PKG/usr/share/ncbi/data |
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# Install the documentation |
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DOCDIR=$PKG/usr/doc/$NAMETGZ-$VERSION |
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mkdir -p $DOCDIR |
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install -m 644 README{,.htm} VERSION $DOCDIR |
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install -m 644 config/README $DOCDIR/README.config |
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install -m 644 network/nsclilib/readme $DOCDIR/README.net-cfg |
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install -m 644 doc/fa2htgs/README $DOCDIR/README.fa2htgs |
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install -m 644 sequin/README $DOCDIR/README.sequin |
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# Install the default config file |
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mkdir -p $PKG/etc/ncbi |
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install -m 644 $CWD/ncbirc $PKG/etc/ncbi/ncbirc.new |
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# Copy slack-desc and doinst.sh files |
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mkdir -p $PKG/install |
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install -m 644 $CWD/slack-desc $PKG/install/slack-desc |
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install -m 755 $CWD/doinst.sh $PKG/install/doinst.sh |
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# Package the tree |
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cd $PKG |
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mkdir -p $OUT |
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PACKAGING=" |
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chown root:root . -R |
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/sbin/makepkg -l y -c n $OUT/$NAMETGZ-$VERSION-$ARCH-$BUILD.tgz |
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rm -rf $PKG |
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rm -rf $TMP/$NAME |
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" |
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if type -p fakeroot ; then |
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echo "$PACKAGING" | fakeroot |
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else |
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su -c "$PACKAGING" |
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fi |
Damien Goutte-Gattat
13 years ago