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ap/ncbi-toolkit: Upgraded to version of 20090302.

slackware-14.2
Damien Goutte-Gattat 13 years ago
parent
commit
994cf1afc6
  1. 172
      ap/ncbi-toolkit/ncbi-toolkit.SlackBuild
  2. BIN
      ap/ncbi-toolkit/ncbi-tools6_6.1.20070822-1.diff.gz
  3. 1
      ap/ncbi-toolkit/ncbi-tools6_6.1.20070822-1.diff.gz.sha1
  4. 2
      ap/ncbi-toolkit/ncbi.tar.gz.sha1

172
ap/ncbi-toolkit/ncbi-toolkit.SlackBuild

@ -21,17 +21,12 @@
#
# 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/$DEBPATCH
WGET=${WGET:-ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20090301/$ARCHIVE}
# Built package infos
NAMETGZ=${NAMETGZ:-ncbi-toolkit}
@ -72,153 +67,62 @@ if [ ! -r $ARCHIVE ]; then
wget "$WGET"
fi
if [ ! -r $DEBPATCH ]; then
wget "$DEBPATCH_URL"
wget "$DEBURL"
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
# Build
cd $TMP
echo "Building $ARCHIVE..."
mkdir ncbi && cd ncbi
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
sed -i "s/^NCBI_LDFLAGS1 =.*/NCBI_LDFLAGS1 = $CPUOPT/
s/^NCBI_OPTFLAG = .*/NCBI_OPTFLAG = $CPUOPT/" \
ncbi/platform/linux-x86.ncbi.mk
./ncbi/make/makedis.csh
# Install binaries and include files
mkdir -p $PKG/usr/include
cp -aL ncbi/bin ncbi/lib $PKG/usr
cp -aL ncbi/include $PKG/usr/include/ncbi
(
cd $PKG/usr/bin
for x in blast psiblast wblast2 ; do
mv $x.REAL $x
mv ${x}_cs.REAL ${x}_cs
done
rm demo* dosimple test*
strip --strip-unneeded * ../lib/*
)
# 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
mkdir -p $PKG/usr/man
cp -aL ncbi/doc/man $PKG/usr/man/man1
find $PKG/usr/man/man1 -type f -exec gzip -9 {} \;
# Install the NCBI data
mkdir -p $PKG/usr/share/ncbi/data
install -m 644 data/* $PKG/usr/share/ncbi/data
# Install shared NCBI data
mkdir -p $PKG/usr/share/ncbi
cp -aL ncbi/data $PKG/usr/share/ncbi
# Install the documentation
DOCDIR=$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
cp ncbi/README{,.htm} ncbi/VERSION $DOCDIR
cp ncbi/config/README $DOCDIR/README.config
cp ncbi/network/nsclilib/readme $DOCDIR/README.net-cfg
cp -aL ncbi/doc/* $DOCDIR
rm -rf $DOCDIR/man
# Install the default config file
mkdir -p $PKG/etc/ncbi
install -m 644 $CWD/ncbirc $PKG/etc/ncbi/ncbirc.new
# Sanitize permission
find $PKG -type d -exec chmod 755 {} \;
find $PKG -type f -exec chmod 644 {} \;
find $PKG/usr/bin -type f -exec chmod 755 {} \;
# Copy slack-desc and doinst.sh files
mkdir -p $PKG/install
install -m 644 $CWD/slack-desc $PKG/install/slack-desc

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ap/ncbi-toolkit/ncbi-tools6_6.1.20070822-1.diff.gz

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1
ap/ncbi-toolkit/ncbi-tools6_6.1.20070822-1.diff.gz.sha1

@ -1 +0,0 @@
ca0a8fd40aa5e3ddf989f42c0f05c75d7f01d1fe ncbi-tools6_6.1.20070822-1.diff.gz

2
ap/ncbi-toolkit/ncbi.tar.gz.sha1

@ -1 +1 @@
5e61f4f73ef52d145d0df86bb00f03f2db833ee9 ncbi.tar.gz
89cfde43423ffcec9588fa9295a875ee22967c63 ncbi.tar.gz

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