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#!/bin/sh
#
# $Id: makeallchives 117677 2008-01-18 17:07:17Z vakatov $
#
#
# Creates all archives from a directory above 'ncbi'
#
# based on mkarchive written by
# J. Epstein, 9/29/95
# modified to work in a distributed environment 3/13/98 (Friday the 13th)
# -Karl Sirotkin
#
PATH=/bin:/usr/bin:$PATH
export PATH
if [ ! -d ncbi ] ; then
echo must be executed above \'ncbi\'
exit 1
fi
if [ ! -d ncbi/build ] ; then
echo must be executed above \'ncbi\' after make
exit 1
fi
datafiles="humrep.fsa lineages.txt sequin.hlp asn2ff.prt bstdt.val \
featdef.val gc.val makerpt.prt objprt.prt pubkey.enc seqcode.val \
sgmlbb.ent taxlist.txt BLOSUM62 KSat.flt KSchoth.flt KSgc.flt \
KShopp.flt KSkyte.flt KSpur.flt KSpyr.flt \
BLOSUM45 BLOSUM80 PAM30 PAM70 KSpcc.mat \
ecnum_ambiguous.txt ecnum_specific.txt UniVec.nhr UniVec.nin UniVec.nsq \
UniVec_Core.nhr UniVec_Core.nin UniVec_Core.nsq"
configfiles="nlmstmanrc sequinrc ncbidtrc"
TOPDIR=`pwd`
configdir=$TOPDIR/ncbi/config/unix
datadir=$TOPDIR/ncbi/data
errmsgdir=$TOPDIR/ncbi/errmsg
sequindoc=$TOPDIR/ncbi/doc/sequin.htm
sequinimages=$TOPDIR/ncbi/doc/images/
#delete the old archive subdir
test -d archive && rm -rf archive
#make sure we have timestamp file
test -f ncbi/VERSION || date > ncbi/VERSION
for i in sequin entrez fa2htgs asn2xml
do
f=""
mkdir -p archive/$i/data
for file in $datafiles
do
ln $datadir/$file archive/$i/data/
done
ln ncbi/VERSION archive/$i/VERSION
# cat > archive/$i/Cn3D.ReadMe <<EOF
#Cn3D is now distributed separately from $i
#To download Cn3D please look at the Cn3D home page or ftp site:
#
#http://www.ncbi.nlm.nih.gov/Structure/cn3d.html
#ftp://ftp.ncbi.nih.gov/cn3d/
#EOF
case "$i" in
entrez)
cat > archive/$i/README.1st <<EOF
If you have not done so already, please refer to the
file at ftp://ftp.ncbi.nih.gov/entrez/README
EOF
f="entrez entrez2 ../doc/firewall.html"
(cd ncbi/build; test -f Nentrez && ln -f Nentrez entrez)
;;
sequin)
f="sequin"
(cd ncbi/build; test -f Psequin && ln -f Psequin sequin)
mkdir -p archive/sequin/errmsg archive/sequin/images
test -d $errmsgdir && ln $errmsgdir/* archive/sequin/errmsg/
test -d $sequinimages && ln $sequinimages/* archive/sequin/images/
test -r $sequindoc && ln $sequindoc archive/sequin/
#for file in $configfiles
#do
# test -r $configdir/$file && ln $configdir/$file archive/sequin/config/
#done
;;
asn2xml)
f="asn2xml ../doc/README.asn2xml ../doc/ncbixml.txt"
#no need in data subdir
rm -rf archive/asn2xml/data
;;
fa2htgs)
f="fa2htgs"
;;
*)
;;
esac
for file in $f
do
if [ -f ./ncbi/build/$file ] ; then
ln ./ncbi/build/$file ./archive/$i/
else
echo "$i: file $file was not built, skipping the archive"
rm -fr ./archive/$i
fi
done
done
#cd back to archive
cd $TOPDIR/archive
case `uname -s` in
SunOS)
case `uname -r` in
4.1*)
platform=sun
;;
*)
if [ `uname -p` = i386 ] ; then
platform=solarisintel
else
platform=solaris
if [ "$SOLARIS_MODE" = "64" ] ; then
platform=solaris64
fi
fi
;;
esac
;;
IRIX*)
case `uname -r` in
4.*)
platform=sgi4
;;
5.*)
platform=sgi5
;;
6.5)
#platform=sgi-mips4
platform=sgi
;;
6.[0-4])
platform=sgi
;;
*)
platform=sgi
;;
esac
;;
Linux)
case `uname -m` in
ppc)
platform=ppclinux
;;
parisc)
platform=hppalinux
;;
alpha)
platform=linux-alpha
;;
x86_64)
platform=linux-x86_64
;;
i?86)
platform=linux-x86
if [ "$LINUX_MODE" = "icc" ] ; then
platform=linux-x86_icc
fi
;;
ia64)
platform=linux-ia64
;;
*)
platform=linux
;;
esac
;;
OSF1)
platform=alphaOSF1
;;
HP-UX)
if [ `uname -m` = ia64 ] ; then
platform=hpux_ia64
else
platform=hpux
fi
;;
QNX)
platform=qnx
;;
FreeBSD)
platform=freebsd
;;
Darwin)
platform=darwin
;;
NetBSD)
platform=netbsd
;;
AIX)
platform=ibm_auto
;;
*)
platform="`uname -s`.`uname -m`"
platform=`echo $platform|tr '[A-Z]' '[a-z]'|tr ' ' '_'`
;;
esac
echo PLATFORM is $platform
pwd
for A in sequin entrez fa2htgs
do
cd $A || continue
#if [ $platform = "linux" ] ; then
# touch README.1st
#fi
if [ $platform = "solaris" ] ; then
touch README.1st
cat >>README.1st <<EOF
As of 5/29/1996, the Solaris executables distributed by NCBI no longer include
a statically-linked Motif library. This is due to the manner in which
Sun distributes Motif libraries. Users of Solaris version 2.4 and higher
will find the runtime shared Motif library on their system. Users of Solaris
version 2.3 and earlier may need to either upgrade their systems or purchase
the Motif library separately.
It may be necessary to set your LD_LIBRARY_PATH environment variable to
point to the directory where this file, libXm.so.3 (the final digit may
vary), appears on your system. E.g.
setenv LD_LIBRARY_PATH /usr/dt/lib
EOF
fi
if [ $platform = "sun" ] ; then
touch README.1st
cat >>README.1st <<EOF
******************************************************************
* ! ! ! W A R N I N G ! ! ! *
* *
* The NCBI Toolkit on *
* Windows 16 bit *
* and *
* SunOS 4.X platforms *
* *
* WILL NO LONGER BE SUPPORTED after May 1, 1999 *
* *
******************************************************************
EOF
fi
if [ $platform = "sgi5" ] ; then
touch README.sgi5
cat >>README.1st <<EOF
*******************************************************************
* ! ! ! W A R N I N G ! ! ! *
* *
* The NCBI Toolkit binaries for IRIX5.X *
* WILL NO LONGER BE SUPPORTED AND BUILT after January 1, 2002 *
* *
*******************************************************************
EOF
fi
#cd back to archive
cd ..
done
for A in sequin entrez fa2htgs asn2xml
do
cd $A || continue
tar cf ../$A.$platform.tar .
rm -f ../$A.$platform.tar.Z
#compress < ../$A.$platform.tar > ../$A.$platform.tar.Z
gzip < ../$A.$platform.tar > ../$A.$platform.tar.gz 2>/dev/null
if [ $? != 0 ] ; then
/usr/ncbi/bin/gzip < ../$A.$platform.tar > ../$A.$platform.tar.gz 2>/dev/null
fi
rm -f ../$A.$platform.tar
# cd back to archive
cd ..
#and remove it
rm -fr $A
done
echo Building blast archive...
BLASTDIR=blast-`cat ../ncbi/demo/.BLAST_VERSION`
mkdir $BLASTDIR
mkdir $BLASTDIR/bin
mkdir $BLASTDIR/data
mkdir $BLASTDIR/doc
for file in blastall blastpgp seedtop formatdb formatrpsdb fastacmd copymat makemat impala megablast blastclust rpsblast bl2seq
do
cp ../ncbi/build/$file $BLASTDIR/bin
done
for file in $datafiles
do
cp ../ncbi/data/$file $BLASTDIR/data
done
for file in bl2seq.html blast.html blastall.html blastclust.html blastdb.html blastftp.html blastpgp.html fastacmd.html filter.html formatdb.html formatrpsdb.html history.html impala.html index.html megablast.html netblast.html rpsblast.html scoring.pdf web_blast.pl
do
cp ../ncbi/doc/blast/$file $BLASTDIR/doc
done
cp ../ncbi/VERSION $BLASTDIR
tar -cpf blast.$platform.tar $BLASTDIR
gzip blast.$platform.tar
rm -rf $BLASTDIR
# end build blast archive
echo Building netblast archive...
mkdir net$BLASTDIR
mkdir net$BLASTDIR/data
mkdir net$BLASTDIR/bin
mkdir net$BLASTDIR/doc
for file in $datafiles
do
cp ../ncbi/data/$file net$BLASTDIR/data
done
cp ../ncbi/doc/firewall.html net$BLASTDIR/doc
cp ../ncbi/doc/blast/netblast.html net$BLASTDIR/doc
cp ../ncbi/bin/blastcl3 net$BLASTDIR/bin
cp ../ncbi/VERSION net$BLASTDIR
tar -cpf netblast.$platform.tar net$BLASTDIR
gzip netblast.$platform.tar
rm -rf net$BLASTDIR
echo Building wwwblast archive...
mkdir blast
cp -r ../ncbi/network/wwwblast/* blast
find blast -type d -name CVS | xargs rm -rf
find blast -type d -name Src | xargs rm -rf
for file in psiblast.REAL psiblast_cs.REAL blast.REAL blast_cs.REAL wblast2.REAL wblast2_cs.REAL bl2bag.cgi nph-viewgif.cgi
do
cp ../ncbi/build/$file blast
done
mkdir -p blast/TmpGifs
chmod 777 blast/TmpGifs
chmod 666 blast/*.log
tar -cpf wwwblast.$platform.tar blast
gzip wwwblast.$platform.tar
rm -rf blast
exit 0
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