ap/ncbi-toolkit: Added.
This commit is contained in:
Damien Goutte-Gattat
parent
981e9d73a7
commit
07ca5d3137
|
|
@ -0,0 +1,12 @@
|
|||
#!/bin/sh
|
||||
config()
|
||||
{
|
||||
NEW="$1"
|
||||
OLD="`dirname $NEW`/`basename $NEW .new`"
|
||||
if [ ! -r $OLD ]; then
|
||||
mv $NEW $OLD
|
||||
elif [ "`cat $OLD | md5sum`" = "`cat $NEW | md5sum`" ]; then
|
||||
rm $NEW
|
||||
fi
|
||||
}
|
||||
config /etc/ncbi/ncbirc.new
|
||||
|
|
@ -0,0 +1,240 @@
|
|||
#!/bin/bash
|
||||
# Build script for Slackware
|
||||
# Damien Goutte-Gattat "gouttegd" <damien.goutte-gattat at e.ujf-grenoble.fr>
|
||||
#
|
||||
# Redistribution and use of this script, with or without modifications, is
|
||||
# permitted provided that the following conditions are met:
|
||||
#
|
||||
# 1. Redistributions of this script must retain the above copyright
|
||||
# notice, this list of conditions and the following disclaimer.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR IMPLIED
|
||||
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
|
||||
# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
||||
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
|
||||
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
|
||||
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
|
||||
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#
|
||||
# Latest ncbi sourcecode is available at:
|
||||
# ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT
|
||||
#
|
||||
# The build process used in this slackbuild is based on the Debian
|
||||
# NCBI-related packages, maintained by Aaron M. Ucko <ucko@debian.org>.
|
||||
|
||||
# Source package infos
|
||||
NAMESRC=${NAMESRC:-ncbi}
|
||||
VERSION=${VERSION:-6.1}
|
||||
ARCHIVE=${ARCHIVE:-$NAMESRC.tar.gz}
|
||||
WGET=${WGET:-ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20070822/$ARCHIVE}
|
||||
DEBPATCH=ncbi-tools6_6.1.20070822-1.diff.gz
|
||||
DEBPATCH_URL=http://ftp.de.debian.org/debian/pool/main/n/ncbi-tools6/$DEBPATCH
|
||||
|
||||
# Built package infos
|
||||
NAMETGZ=${NAMETGZ:-ncbi-toolkit}
|
||||
BUILD=${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
|
||||
if [ ! -r $DEBPATCH ]; then
|
||||
wget "$DEBPATCH_URL"
|
||||
fi
|
||||
sha1sum -c $ARCHIVE.sha1
|
||||
sha1sum -c $DEBPATCH.sha1
|
||||
NAME=$(tar ft $ARCHIVE | head -1 | cut -d / -f 1)
|
||||
|
||||
# Extract archive and apply the Debian patch
|
||||
cd $TMP
|
||||
echo "Building $ARCHIVE..."
|
||||
tar xf $CWD/$ARCHIVE
|
||||
cd $NAME
|
||||
zcat $CWD/$DEBPATCH | patch -p1
|
||||
|
||||
# Compile
|
||||
|
||||
export NCBI_VERSION=$VERSION
|
||||
export NCBI_VERSION_MAJOR=$(echo $VERSION | cut -d. -f1)
|
||||
export NCBI_VERSION_MINOR=$(echo $VERSION | cut -d. -f2)
|
||||
export BLAST_VERSION=$(cat demo/.BLAST_VERSION)
|
||||
export NCBI_LBSM_SRC=ncbi_lbsmd_stub.c
|
||||
export NCBI_LBSM_OBJ=ncbi_lbsmd_stub.o
|
||||
export LD_LIBRARY_PATH=$TMP/$NAME/shlib:$LD_LIBRARY_PATH
|
||||
|
||||
cd build
|
||||
ln -s ../make/*.unx .
|
||||
ln -s ../make/ln-if-absent .
|
||||
mv makeall.unx makefile
|
||||
|
||||
pmake all LCL=lnx CC=gcc RAN=ranlib \
|
||||
OTHERLIBS=-lm VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG=-DWIN_MOTIF \
|
||||
NCBI_LINKINGLIBDIR="../shlib -L../lib" \
|
||||
CFLAGS1="-c $CPUOPT -D_PNG -fPIC" \
|
||||
LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \
|
||||
LIB30=libncbicn3d.a LIB45=libddvlib.a \
|
||||
LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a
|
||||
|
||||
pmake -f makenet.unx LCL=lnx CC=gcc RAN=ranlib \
|
||||
OTHERLIBS=-lm VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG=-DWIN_MOTIF \
|
||||
NCBI_LINKINGLIBDIR="../shlib -L../lib" \
|
||||
CFLAGS1="-c $CPUOPT -fPIC" \
|
||||
NETENTREZVERSION=2.02c2ASN1SPEC6 \
|
||||
BLIB31=libvibnet.a OGLLIBS="-lGLU -lGL -lpng" \
|
||||
all libncbimla.a libnetblast.a libncbitxc2.a libncbiid1.a shlib
|
||||
|
||||
pmake clean
|
||||
|
||||
pmake all LCL=lnx CC=gcc RAN=ranlib \
|
||||
OTHERLIBS=-lm VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG=-DWIN_MOTIF \
|
||||
NCBI_LINKINGLIBDIR="../shlib -L../lib" \
|
||||
CFLAGS1="-c $CPUOPT -D_PNG" \
|
||||
LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \
|
||||
LIB30=libncbicn3d.a LIB45=libddvlib.a \
|
||||
LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a
|
||||
|
||||
pmake -f makedemo.unx LCL=lnx CC=gcc RAN=ranlib \
|
||||
OTHERLIBS=-lm VIBLIBS= VIBFLAG= \
|
||||
NCBI_LINKINGLIBDIR="../shlib -L../lib" \
|
||||
CFLAGS1="-c $CPUOPT" \
|
||||
LIB50=-lpcre
|
||||
|
||||
rm -f blast blastall blastall_old blastpgp seedtop megablast rpsblast \
|
||||
blastclust
|
||||
|
||||
pmake -f makedemo.unx LCL=lnx CC=gcc RAN=ranlib \
|
||||
OTHERLIBS=-lm THREAD_OBJ=ncbithr.o THREAD_OTHERLIBS=-lpthread \
|
||||
NCBI_LINKINGLIBDIR="../shlib -L../lib" \
|
||||
VIBLIBS= VIBFLAG= \
|
||||
blast blastall blastall_old blastpgp seedtop megablast rpsblast \
|
||||
blastclust
|
||||
|
||||
pmake -f makenet.unx LCL=lnx CC=gcc RAN=ranlib \
|
||||
OTHERLIBS=-lm VIBFLAG=-DWIN_MOTIF \
|
||||
NCBI_LINKINGLIBDIR="../shlib -L../lib" \
|
||||
CFLAGS1="-c $CPUOPT" \
|
||||
THREAD_OBJ=ncbithr.o THREAD_OTHERLIBS=-lpthread \
|
||||
NETENTREZVERSION=2.02c2ASN1SPEC6 \
|
||||
BLIB31=libvibnet.a OGLLIBS= VIBLIBS= \
|
||||
VIB="Psequin sbtedit udv ddv blastcl3 idfetch bl2seq asn2gb tbl2asn \
|
||||
gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml cleanasn \
|
||||
insdseqget nps2gps spidey trna2sap trna2tbl Cn3D"
|
||||
|
||||
# Prepare the package tree
|
||||
cd $TMP/$NAME
|
||||
mkdir -p $PKG/usr/lib
|
||||
install -m 644 lib/* shlib/*.so.$VERSION $PKG/usr/lib
|
||||
for x in ncbiacc ncbiCacc netentr; do
|
||||
rm -f $PKG/usr/lib/lib$x.so.$VERSION
|
||||
ln -s libncbiNacc.so.$NCBI_VERSION_MAJOR \
|
||||
$PKG/usr/lib/lib$x.so.$NCBI_VERSION_MAJOR
|
||||
ln -s libncbiNacc.so $PKG/usr/lib/lib$x.so
|
||||
done
|
||||
for x in ncbicn3d vibrant; do
|
||||
rm -f $PKG/usr/lib/lib$x.so.$VERSION
|
||||
ln -s lib${x}OGL.so.$NCBI_VERSION_MAJOR \
|
||||
$PKG/usr/lib/lib$x.so.$NCBI_VERSION_MAJOR
|
||||
ln -s lib${x}OGL.so $PKG/usr/lib/lib$x.so
|
||||
done
|
||||
cd $PKG/usr/lib
|
||||
for f in *.so.$VERSION; do
|
||||
base=$(basename $f .so.$VERSION)
|
||||
ln -s $f $base.so.$NCBI_VERSION_MAJOR
|
||||
ln -s $f $base.so
|
||||
done
|
||||
|
||||
cd $TMP/$NAME
|
||||
mkdir -p $PKG/usr/include/ncbi
|
||||
cp -LRp include/* $PKG/usr/include/ncbi
|
||||
cd $PKG/usr/include/ncbi
|
||||
rm -f FSpCompat.h FullPath.h More*.h Optimization*.h pcre*.h
|
||||
find . -type f | xargs chmod 644
|
||||
|
||||
cd $TMP/$NAME
|
||||
mkdir -p $PKG/usr/bin
|
||||
install $(find build -type f -perm +111 -print) $PKG/usr/bin
|
||||
install -m 755 debian/vibrate $PKG/usr/bin
|
||||
rm -f $PKG/usr/bin/{dosimple,ncbisort,cdscan,entrcmd,*test*,*demo*}
|
||||
mv $PKG/usr/bin/Cn3D $PKG/usr/bin/Cn3D-3.0
|
||||
mv $PKG/usr/bin/blast $PKG/usr/bin/blast2
|
||||
|
||||
# Strip binaries
|
||||
find $PKG | xargs file | grep "ELF 32-bit LSB" | cut -d : -f 1 | \
|
||||
xargs strip --strip-unneeded 2> /dev/null
|
||||
|
||||
# Install and compress man pages
|
||||
mkdir -p $PKG/usr/man/man1
|
||||
install -m 644 doc/man/* $PKG/usr/man/man1
|
||||
install -m 644 debian/man/* $PKG/usr/man/man1
|
||||
rm -f $PKG/usr/man/man1/entrcmd.1
|
||||
find $PKG/usr/man/man1 -type f | xargs gzip -9 2> /dev/null
|
||||
|
||||
# Install the NCBI data
|
||||
mkdir -p $PKG/usr/share/ncbi/data
|
||||
install -m 644 data/* $PKG/usr/share/ncbi/data
|
||||
|
||||
# Install the documentation
|
||||
DOCDIR=$PKG/usr/doc/$NAMETGZ-$VERSION
|
||||
mkdir -p $DOCDIR
|
||||
install -m 644 README{,.htm} VERSION $DOCDIR
|
||||
install -m 644 config/README $DOCDIR/README.config
|
||||
install -m 644 network/nsclilib/readme $DOCDIR/README.net-cfg
|
||||
install -m 644 doc/fa2htgs/README $DOCDIR/README.fa2htgs
|
||||
install -m 644 sequin/README $DOCDIR/README.sequin
|
||||
|
||||
# Install the default config file
|
||||
mkdir -p $PKG/etc/ncbi
|
||||
install -m 644 $CWD/ncbirc $PKG/etc/ncbi/ncbirc.new
|
||||
|
||||
# Copy slack-desc and doinst.sh files
|
||||
mkdir -p $PKG/install
|
||||
install -m 644 $CWD/slack-desc $PKG/install/slack-desc
|
||||
install -m 755 $CWD/doinst.sh $PKG/install/doinst.sh
|
||||
|
||||
# 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 $TMP/$NAME
|
||||
"
|
||||
if type -p fakeroot ; then
|
||||
echo "$PACKAGING" | fakeroot
|
||||
else
|
||||
su -c "$PACKAGING"
|
||||
fi
|
||||
Binary file not shown.
|
|
@ -0,0 +1 @@
|
|||
ca0a8fd40aa5e3ddf989f42c0f05c75d7f01d1fe ncbi-tools6_6.1.20070822-1.diff.gz
|
||||
|
|
@ -0,0 +1 @@
|
|||
5e61f4f73ef52d145d0df86bb00f03f2db833ee9 ncbi.tar.gz
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
[NCBI]
|
||||
DATA=/usr/share/ncbi/data
|
||||
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
|-----handy-ruler------------------------------------------------------|
|
||||
ncbi-toolkit: ncbi-toolkit (NCBI Software Development Toolkit)
|
||||
ncbi-toolkit:
|
||||
ncbi-toolkit: The NCBI Software Development Toolkit has been used for the
|
||||
ncbi-toolkit: production and distribution of GenBank, Entrez, BLAST, and related
|
||||
ncbi-toolkit: services by NCBI. It is freely available without restriction to
|
||||
ncbi-toolkit: facilitate the use of NCBI by the scientific community.
|
||||
ncbi-toolkit:
|
||||
ncbi-toolkit:
|
||||
ncbi-toolkit:
|
||||
ncbi-toolkit:
|
||||
ncbi-toolkit:
|
||||
|
||||
Loading…
Reference in New Issue