ap/ncbi-toolkit: Do not attempt to build X11 apps anymore.

ap/ncbi-toolkit/build-fixes.diff

@@ -0,0 +1,40 @@
+diff -Naur ncbi.orig/ncbi/corelib/ncbienv.c ncbi/ncbi/corelib/ncbienv.c
+--- ncbi.orig/ncbi/corelib/ncbienv.c	2007-05-04 15:43:59.000000000 +0200
++++ ncbi/ncbi/corelib/ncbienv.c	2009-03-27 01:37:01.000000000 +0100
+@@ -812,6 +812,8 @@
+     if (fp == NULL) {
+       path[0] = '\0';
+       pth = getenv ("NCBI");
++      if (pth == NULL)
++        pth = "/etc/ncbi";
+       if (pth != NULL) {
+         Nlm_FileBuildPath(path, pth, str + 1);
+         fp = Ncbienv_FileOpen (path, "r");
+diff -Naur ncbi.orig/ncbimake/makedis.csh ncbi/ncbi/make/makedis.csh
+--- ncbi.orig/ncbi/make/makedis.csh	2008-12-30 16:15:10.000000000 +0100
++++ ncbi/ncbi/make/makedis.csh	2009-03-27 01:39:23.000000000 +0100
+@@ -342,8 +342,8 @@
+ #
+ 
+ #uncomment two following lines to don't build X11 apps
+-#set HAVE_OGL=0
+-#set HAVE_MOTIF=0
++set HAVE_OGL=0
++set HAVE_MOTIF=0
+ 
+ # if $OPENGL_TARGETS (in <platform>.ncbi.mk) is defined, 
+ # then add the appropriate flags, libraries, and binaries for OpenGL apps
+diff -Naur ncbi/ncbi.orig/platform/linux-x86.ncbi.mk ncbi/ncbi/platform/linux-x86.ncbi.mk
+--- ncbi.orig/ncbi/platform/linux-x86.ncbi.mk	2009-02-04 15:24:03.000000000 +0100
++++ ncbi/ncbi/platform/linux-x86.ncbi.mk	2009-03-27 01:38:18.000000000 +0100
+@@ -11,8 +11,8 @@
+ NCBI_AR=ar
+ NCBI_CC = gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_GNU_SOURCE
+ NCBI_CFLAGS1 = -c
+-NCBI_LDFLAGS1 = -O3 -mcpu=pentium4
+-NCBI_OPTFLAG = -O3 -mcpu=pentium4
++NCBI_LDFLAGS1 = -O2 -march=i686 -mtune=i686
++NCBI_OPTFLAG = -O2 -march=i686 -mtune=i686
+ NCBI_BIN_MASTER = /home/coremake/ncbi/bin
+ NCBI_BIN_COPY = /home/coremake/ncbi/bin
+ NCBI_INCDIR = /home/coremake/ncbi/include

ap/ncbi-toolkit/ncbi-toolkit.SlackBuild

@@ -30,7 +30,7 @@ WGET=${WGET:-ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20090301/$ARCHIVE}
 
 # Built package infos
 NAMETGZ=${NAMETGZ:-ncbi-toolkit}
-BUILD=${BUILD:-1GGD}
+BUILD=${BUILD:-2GGD}
 ARCH=${ARCH:-i486}
 TARGET=${TARGET:-i486}
 
@@ -52,23 +52,10 @@ if [ ! -d $TMP ]; then
     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 $DEBPATCH ]; then
-    wget "$DEBURL"
-fi
 sha1sum -c $ARCHIVE.sha1
 NAME=$(tar ft $ARCHIVE | head -1 | cut -d / -f 1)
 
@@ -77,28 +64,26 @@ cd $TMP
 echo "Building $ARCHIVE..."
 mkdir ncbi && cd ncbi
 tar xf $CWD/$ARCHIVE
-sed -i "s/^NCBI_LDFLAGS1 =.*/NCBI_LDFLAGS1 = $CPUOPT/
-        s/^NCBI_OPTFLAG = .*/NCBI_OPTFLAG = $CPUOPT/" \
-        ncbi/platform/linux-x86.ncbi.mk
+patch -p 1 < $CWD/build-fixes.diff
 ./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/bin $PKG/usr/bin
+rm $PKG/usr/bin/{demo*,dosimple,test*}
+mv $PKG/usr/bin/wblast2.REAL $PKG/usr/bin/wblast2
+mv $PKG/usr/bin/wblast2_cs.REAL $PKG/usr/bin/wblast2_cs
+cp -aL ncbi/lib $PKG/usr/lib
+strip --strip-unneeded $PKG/usr/bin/* $PKG/usr/lib/*
 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/*
-)
+rm $PKG/usr/include/ncbi/{cn3d*,pcre*,vib*}
 
 # Install and compress man pages
 mkdir -p $PKG/usr/man
 cp -aL ncbi/doc/man $PKG/usr/man/man1
+rm $PKG/usr/man/man1/{Psequin.1,asnval.1,cleanasn.1,ddv.1,entrez2.1,\
+fmerge.1,gbseqget.1,insdseqget.1,nps2gps.1,sortbyquote.1,spidey.1,\
+trna2sap.1,trna2tbl.1,udv.1}
 find $PKG/usr/man/man1 -type f -exec gzip -9 {} \;
 
 # Install shared NCBI data
@@ -118,7 +103,7 @@ rm -rf $DOCDIR/man
 mkdir -p $PKG/etc/ncbi
 install -m 644 $CWD/ncbirc $PKG/etc/ncbi/ncbirc.new
 
-# Sanitize permission
+# Sanitize permissions
 find $PKG -type d -exec chmod 755 {} \;
 find $PKG -type f -exec chmod 644 {} \;
 find $PKG/usr/bin -type f -exec chmod 755 {} \;