ap/ncbi-toolkit: Added.

ap/ncbi-toolkit/doinst.sh

@@ -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

ap/ncbi-toolkit/ncbi-toolkit.SlackBuild

@@ -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

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

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

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

@@ -0,0 +1 @@
+5e61f4f73ef52d145d0df86bb00f03f2db833ee9  ncbi.tar.gz

ap/ncbi-toolkit/ncbirc

@@ -0,0 +1,3 @@
+[NCBI]
+DATA=/usr/share/ncbi/data
+

ap/ncbi-toolkit/slack-desc

@@ -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: 
+