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

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

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

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

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

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