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|
#!/bin/csh -f
#
# $Id: makedis.csh 155379 2009-03-23 17:10:14Z coulouri $
#
## PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
# Author: Karl Sirotkin <sirotkin@ncbi.nlm.nih.gov>
#
# IBM AIX section: cpsosa@us.ibm.com Jun-2001
#
# Script to untar and make the NCBI toolkit on Solaris.
#
# NOTE: use "/bin/tcsh" above if "/bin/csh" is absent (e.g. on QNX OS)
set MFLG=""
if ("X$1" == "X-n") then
set MFLG="-n"
shift
endif
set tar_file = $1
set cwd = `pwd`
# do we need to extract the tar archive?
if ( "X$tar_file" != "X" && "$tar_file" != "-") then
if (! -r "$tar_file") then
echo Unable to find the file "$tar_file"
exit 1
endif
if (-d "ncbi") then
echo "ncbi directory already exists, please remove or rename it"
exit 2
endif
ls -l $tar_file
tar xvf $tar_file
else
# make sure that ncbi/build directory exists
if ( ! -d "ncbi/build" ) then
echo 'ncbi/build directory should exist. Did you extract ncbi.tar.Z?'
exit 2
endif
endif
set os=`uname -s`
#by default any Unix has Motif installed. In case of Linux do a check later.
set HAVE_MOTIF=1
#darwin will use native Mac GUI
set HAVE_MAC=0
#we will try to build OpenGL version of vibrant
set HAVE_OGL=1
switch ($os)
case SunOS:
switch (`uname -r`)
case "4.1*":
set platform=sun
breaksw
default:
if ( `uname -p` == i386 ) then
set platform=solarisintel
if ("$?CC" == 1) then
if ("$CC" == "gcc") then
set platform=solaris-gcc
endif
endif
else
set platform=solaris
if ("$?CC" == 1) then
if ("$CC" == "gcc") then
set platform=solaris-gcc
endif
else if ("$?SOLARIS_MODE" == 1) then
if ("$SOLARIS_MODE" == "64") then
set platform=solaris64
endif
endif
endif
breaksw
endsw
set HAVE_OGL=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 /usr/openwin/include )
if (-d $i/GL) then
set HAVE_OGL=1
echo OpenGL found at $i/GL
break
endif
end
breaksw
case IRIX*:
switch (`uname -r`)
case "4.*":
set platform=sgi4
breaksw
case "5.*":
set platform=sgi5
breaksw
case "6.5":
#set platform=sgi-mips4
set platform=sgi
breaksw
case "6.[0-4]":
set platform=sgi
breaksw
default:
set platform=sgi
breaksw
endsw
breaksw
case OSF1:
set platform=alphaOSF1
set HAVE_MOTIF=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 )
if (-d $i/Xm) then
set HAVE_MOTIF=1
echo Motif found at $i/Xm
break
endif
end
breaksw
case Linux:
case GNU/Linux:
lsb_release -a
echo "libs version is:"
ls -l /lib/libc.so*
echo "the gcc version is:"
gcc -v
switch (`uname -m`)
case "ia64":
if (-e `which icc`) then
set platform=linux_ecc
else
set platform=linux
endif
breaksw
case "ppc":
set platform=ppclinux
breaksw
case "parisc":
set platform=hppalinux
breaksw
case "i?86":
set platform=linux-x86
if ("$?LINUX_MODE" == 1) then
if ("$LINUX_MODE" == "icc") then
switch (`icc -dumpversion`)
case "9.*":
case "[1-9][0-9]*":
set platform=linux_icc9
breaksw
default:
set platform=linux_icc
breaksw
endsw
endif
endif
breaksw
case "alpha":
set platform=linux-alpha
breaksw
case "ppc64":
set platform=linux-power
breaksw
default:
if (-d /usr/X11R6/lib64) then
set platform=linux64
else
set platform=linux
endif
if ("$?LINUX_MODE" == 1) then
if ("$LINUX_MODE" == "icc") then
set platform=${platform}_icc9
endif
endif
breaksw
endsw
#check do we have Motif on linux installed
set HAVE_MOTIF=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 )
if (-d $i/Xm) then
set HAVE_MOTIF=1
echo Motif found at $i/Xm
echo "Warning: Motif version 1.2 is recommended"
break
endif
end
#check do we have OpenGL installed
set HAVE_OGL=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 /usr/openwin/include )
if (-d $i/GL) then
set HAVE_OGL=1
echo OpenGL found at $i/GL
break
endif
end
breaksw
case FreeBSD:
set platform=freebsd
set HAVE_MOTIF=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 )
if (-d $i/Xm) then
set HAVE_MOTIF=1
echo Motif found at $i/Xm
break
endif
end
breaksw
case Darwin:
set platform=darwin
if ("$?DARWIN_MODE" == 1) then
if ("$DARWIN_MODE" == "universal") then
set platform=darwin-univ
endif
endif
set HAVE_MOTIF=0
set HAVE_MAC=1
breaksw
case NetBSD:
set platform=netbsd
set HAVE_MOTIF=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 )
if (-d $i/Xm) then
set HAVE_MOTIF=1
echo Motif found at $i/Xm
break
endif
end
breaksw
case AIX:
set arch=`uname -M`
set platform=ibm_auto
if ("$?AIX_MODE" == 1) then
if ("$AIX_MODE" == "64") then
echo "64-bit mode build was selected for AIX"
set platform=ibm_auto64
endif
endif
echo "AIX machine is $arch"
set HAVE_MOTIF=0
foreach i (/usr/X11R6/include /usr/X11R6/include/X11 /usr/include \
/usr/include/X11 )
if (-d $i/Xm) then
set HAVE_MOTIF=1
echo Motif found at $i/Xm
break
endif
end
breaksw
case HP-UX:
switch (`uname -m`)
case "ia64":
set platform=hpux_ia64
breaksw
case "9000/800":
set platform=hpux
breaksw
default:
set platform=hpux
breaksw
endsw
breaksw
case QNX:
#uname -a: QNX qnxrulez 6.1.0 2001/06/25-15:31:48edt x86pc x86
set platform=qnx
breaksw
default:
echo Platform not found : `uname -a`
goto BADPLATFORM
breaksw
endsw
echo platform is $platform
uname -a
set NCBI_DOT_MK = ncbi/platform/${platform}.ncbi.mk
if (! -r "$NCBI_DOT_MK") then
goto BADPLATFORM
endif
set noglob
# take the file $NCBI_DOT_MK and convert it to be suitable for csh eval:
# (1) remove comments at the beginning of the lines
# (2) change variable referenses to be in curly brackets - $AAA -> ${AAA}
# (3) remove excessive spaces around the equal sign
# (4) change Makefile assignments to csh ones: AAA=bb cc -> setenv AAA "bb cc"
eval `sed -e 's/^ *#.*//g' -e 's/\$(\([a-zA-Z_]*\))/\${\1}/g' -e 's/ *= */=/g' -e 's/^\([^=]*\)=\(.*\)$/setenv \1 "\2";/' < $NCBI_DOT_MK`
unset noglob
# disable assert() unless ENABLE_ASSERT is set
if ("$?ENABLE_ASSERT" == 0) then
set NCBI_OPTFLAG="-DNDEBUG $NCBI_OPTFLAG"
echo "Disabling assert()."
else
echo "Enabling assert()."
endif
cd ncbi/build
ln -s ../make/*.unx .
ln -s ../make/ln-if-absent .
mv makeall.unx makefile
if ( -r ../demo/.BLAST_VERSION ) then
echo BLAST version is `cat ../demo/.BLAST_VERSION`
endif
# Inherited to this system is the requirement to use:
# TO USE VIBRANT
# to have for makeall, this line
# LIB30=libncbicn3d.a LIB28=libvibgif.a LIB4=libvibrant.a LIB20=libncbidesk.a
# LIB45=libddvlib.a and for the makenet, this symbol
# BLIB31=libvibnet.a
#
#uncomment two following lines to don't build X11 apps
#set HAVE_OGL=0
#set HAVE_MOTIF=0
# if $OPENGL_TARGETS (in <platform>.ncbi.mk) is defined,
# then add the appropriate flags, libraries, and binaries for OpenGL apps
if ("$?OPENGL_TARGETS" == "1" && "$HAVE_OGL" == "1" ) then
set OGL_NCBI_LIBS="$OPENGL_NCBI_LIBS"
set OGL_INCLUDE="$OPENGL_INCLUDE"
set OGL_LIBS="$OPENGL_LIBS"
set OGL_TARGETS="$OPENGL_TARGETS"
else
set OGL_NCBI_LIBS=""
set OGL_INCLUDE=""
set OGL_LIBS=""
set OGL_TARGETS=""
endif
# if LIBPNG_DIR and ZLIB_DIR (in <platform>.ncbi.mk) are defined,
# then add the appropriate flags and libraries for PNG support
if ("$?LIBPNG_DIR" == "1" && "$?ZLIB_DIR" == "1") then
set PNG_INCLUDE="-D_PNG -I$LIBPNG_DIR -I$ZLIB_DIR"
set PNG_LIBS="$LIBPNG_DIR/libpng.a $ZLIB_DIR/libz.a"
else
set PNG_INCLUDE=""
set PNG_LIBS=""
endif
set VIBWWWBLAST=(psiblast.REAL psiblast_cs.REAL blast.REAL blast_cs.REAL)
set NONVIBWWWBLAST=(nph-viewgif.cgi wblast2.REAL wblast2_cs.REAL bl2bag.cgi)
set WWWBLAST=($VIBWWWBLAST $NONVIBWWWBLAST)
if ( "$HAVE_MOTIF" == 1 ) then
set ALL_VIB=(LIB30=libncbicn3d.a \
LIB28=libvibgif.a \
LIB4=libvibrant.a \
LIB20=libncbidesk.a \
LIB45=libddvlib.a \
$OGL_NCBI_LIBS \
VIBFLAG=\"$NCBI_VIBFLAG\" \
VIBLIBS=\"$NCBI_DISTVIBLIBS\")
#By default we don't need to build demo programs with vibrant lib
#set DEMO_VIB=(LIB4=-lvibrant \
# VIBLIBS=\"$NCBI_DISTVIBLIBS\" \
# VIBFLAG=\"$NCBI_VIBFLAG\")
set DEMO_VIB=()
set NET_VIB=(BLIB31=libvibnet.a \
VIBLIBS=\"$NCBI_DISTVIBLIBS\" \
OGLLIBS=\"$OGL_LIBS $PNG_LIBS\" \
VIBFLAG=\"$NCBI_VIBFLAG\" \
VIB=\"Psequin sbtedit Nentrez udv ddv blastcl3 taxblast \
idfetch bl2seq asn2gb tbl2asn gene2xml entrez2 gbseqget \
$WWWBLAST $OGL_TARGETS\")
else if ( "$HAVE_MAC" == 1 ) then
set ALL_VIB=(LIB30=libncbicn3d.a \
LIB28=libvibgif.a \
LIB4=libvibrant.a \
LIB20=libncbidesk.a \
LIB45=libddvlib.a \
$OGL_NCBI_LIBS \
VIBFLAG=\"$NCBI_VIBFLAG\" \
VIBLIBS=\"$NCBI_DISTVIBLIBS\")
#By default we don't need to build demo programs with vibrant lib
#set DEMO_VIB=(LIB4=-lvibrant \
# VIBLIBS=\"$NCBI_DISTVIBLIBS\" \
# VIBFLAG=\"$NCBI_VIBFLAG\")
set DEMO_VIB=()
set NET_VIB=(BLIB31=libvibnet.a \
VIBLIBS=\"$NCBI_DISTVIBLIBS\" \
OGLLIBS=\"$OGL_LIBS $PNG_LIBS\" \
VIBFLAG=\"$NCBI_VIBFLAG\" \
VIB_POST_LINK=\"../make/make-mac-bundle\" \
VIB=\"Psequin sbtedit udv ddv blastcl3 taxblast \
idfetch bl2seq asn2gb tbl2asn gene2xml entrez2 gbseqget $WWWBLAST \")
else # no Motif, build only ascii-based applications
set OGL_NCBI_LIBS=""
set OGL_INCLUDE=""
set OGL_LIBS=""
set OGL_TARGETS=""
set ALL_VIB=()
set DEMO_VIB=()
set NET_VIB=(VIB=\"blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn gene2xml $NONVIBWWWBLAST \")
endif
set CMD='make $MFLG \
CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \
RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all'
eval echo $CMD
eval echo $CMD | sh
set make_stat = $status
if ( $make_stat != 0 ) then
cat <<EoF
Fatal error building NCBI core libraries.
Please be sure that you have X11 and Motif libraries installed.
The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful.
EoF
exit 1
endif
set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $DEMO_VIB'
eval echo $CMD
eval echo $CMD | sh
set demo_stat = $status
#
# In case platform supports multi-threading, remake the apps which
# should be multithreaded, if at all possible.
# Might repeat what is done above on some platforms.
#
set mtapps = "blastall blastpgp seedtop megablast rpsblast blastclust"
rm -f $mtapps
set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" \
THREAD_OBJ=$NCBI_THREAD_OBJ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
$DEMO_VIB $mtapps'
eval echo $CMD
eval echo $CMD | sh
set threaded_demo_stat = $status
if ("$?NCBI_MT_OTHERLIBS" == "1") then
set CMD='make $MFLG -f makenet.unx \
CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
THREAD_OBJ=$NCBI_THREAD_OBJ \
THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB'
else
set CMD='make $MFLG -f makenet.unx \
CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB'
endif
eval echo $CMD
eval echo $CMD | sh
set net_stat = $status
if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
cat <<EOF
#######
# ##### ##### #### #####
# # # # # # # # #
##### # # # # # # # #
# ##### ##### # # #####
# # # # # # # # #
####### # # # # #### # #
EOF
exit 1
else
# we are in ncbi/build directory now. Let us make the VERSION file
echo "Put the date stamp to the file ../VERSION"
echo "The executable files were built on `date`" > ../VERSION
echo "The version number of each individual application" >> ../VERSION
echo "may be found in the appropriate documentation files in ./ncbi/doc/" >> ../VERSION
echo "uname -a ouput is: `uname -a`" >> ../VERSION
foreach i ( Nentrez Psequin sbtedit asn2ff asn2xml asn2gb asn2idx asndhuff asntool bl2seq \
blastall blastall_old blastcl3 blastclust blastpgp cdscan checksub \
copymat ddv demo_regexp demo_regexp_grep dosimple entrcmd entrez \
errhdr fa2htgs fastacmd findspl fmerge formatdb formatrpsdb getfeat \
getmesh getpub getseq gil2bin idfetch impala indexpub makemat makeset \
megablast ncbisort netentcf rpsblast seedtop seqtest sequin entrez2 \
tbl2asn gene2xml test_regexp testcore testobj testval udv vecscreen Cn3D \
blast debruijn taxblast $WWWBLAST )
if ( -x ./$i ) then
rm -rf ../bin/$i ../bin/$i.app
if ( $os == "Darwin" ) then
/Developer/Tools/Rez Carbon.r -o $i
if ( -x ./$i.app ) then
cp -pr ./$i.app ../bin/
endif
endif
ln ./$i ../bin/
endif
end
echo '*********************************************************'
echo '*The new binaries are located in ./ncbi/build/ directory*'
echo '*********************************************************'
exit 0
endif
BADPLATFORM:
cat << EoF
Your platform is not supported.
To port ncbi toolkit to your platform consult
the files ./ncbi/platform/*.ncbi.mk
The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be useful.
EoF
exit 0
|