454 lines
9.8 KiB
Text
454 lines
9.8 KiB
Text
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#! /bin/csh -f
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#
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# staden_install - version 2.4
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#
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# This is a prototype installation program.
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#
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# 9 March 1992
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# Modified for installation on Sun, Alliant, etc
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# No longer install 2rs
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#
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# 20 November 1992
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# Now includes convert, cop, frog, getMCH and scf
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#
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# 25 November 1992
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# SGI supported
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#
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# 19 May 1993
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# DEC Alpha, Solaris supported
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#
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# Written by sd@uk.ac.cam.mrc-lmb
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#
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# prelim
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set prog = $0 ; set prog = $prog:t
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# Machines supported: al sun dec sgi alpha solaris
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#set MACHINE = `echo $prog | sed 's/.*-//'`
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set MACHINE = solaris
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# For local (MRC-LMB) setup only
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#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
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set LOCAL = NO
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echo ""
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echo -n "Staden Package installation procedure - "
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switch (${MACHINE})
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case "al":
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echo "Alliant FX/2800 Concentrix version"
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set MAKE = "make -sk"
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breaksw
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case "sun":
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echo "SunOS version"
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set MAKE = "make -sk"
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breaksw
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case "dec":
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echo "DEC Ultrix (mips) version"
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set MAKE = "gmake -sk"
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breaksw
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case "sgi":
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echo "Silicon Graphics Iris version"
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set MAKE = "gmake -sk"
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breaksw
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case "alpha":
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echo "DEC Alpha OSF/1 version"
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set MAKE = "gmake -sk"
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breaksw
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case "solaris":
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echo "Solaris version"
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set MAKE = "make -sk"
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breaksw
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default:
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echo "Panic. Unknown version"
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exit 1
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endsw
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echo ""
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echo "* starting initialization...please wait."
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echo ""
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# Binary fork of source directory
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if ($LOCAL == "YES") then
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set DIR_BINARIES = ${MACHINE}-binaries
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set DIR_PROGS = ${MACHINE}-bin
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else
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set DIR_BINARIES = .
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set DIR_PROGS = bin
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set MAKE = "$MAKE -f makefile-${MACHINE}"
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endif
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init:
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# Set useful shell variables
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set YES="YES";
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set NO="NO"
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# set/unset some .cshrc envs.
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unset noclobber
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set noglob
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# set interrupt trap
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onintr end_failure
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# Make dir command
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set MKDIR = "mkdir"
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# Copy command
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set CP = "cp -p"
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# Install command
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#set INSTALL = "install"
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#set INSTALL = "mv"
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set INSTALL = "cp"
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# Set up default responses
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set DEF_STADEN_ROOT = `pwd`
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set DEF_REQ_NONX = "$YES"
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set DEF_REQ_X = "$YES"
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set DEF_REQ_TED = "$YES"
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set DEF_REQ_MISC = "$YES"
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# directories
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set DIR_SRC = $DEF_STADEN_ROOT/src
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set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
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set DIR_MISC = $DIR_SRC/Misc
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set DIR_STADEN = $DIR_SRC/staden
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set DIR_TED = $DIR_SRC/ted
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set DIR_ABI = $DIR_SRC/abi
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set DIR_ALF = $DIR_SRC/alf
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set DIR_BAP = $DIR_SRC/bap
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set DIR_OSP = $DIR_SRC/bap/osp-bits
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set DIR_CONVERT = $DIR_SRC/convert
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set DIR_COP = $DIR_SRC/cop
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set DIR_FROG = $DIR_SRC/frog
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set DIR_GETMCH = $DIR_SRC/getMCH
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set DIR_SCF = $DIR_SRC/scf
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main:
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preamble:
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echo ""
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echo ""
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echo "* Please answer the following questions."
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echo " Default answers to questions are given in square brackets."
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echo " If you require help at any stage respond with a ? to the question."
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echo ""
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ask_staden_root:
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set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
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ask_require_nonx_progs:
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echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
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set ANS_REQ_NONX = $<
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if ("$ANS_REQ_NONX" == "?") then
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echo "* If you do not have X windows on your system you will require"
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echo " these. However, you will require Tektronics terminal emulation."
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echo " If you do not require all of the non-X programs, you should abort"
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echo " and manually make the ones you require."
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echo ""
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goto ask_require_nonx_progs
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else if ("$ANS_REQ_NONX" != "") then
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if ("$ANS_REQ_NONX" =~ [yY]*) then
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set ANS_REQ_NONX=$YES
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else if ("$ANS_REQ_NONX" =~ [nN]*) then
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set ANS_REQ_NONX=$NO
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else
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goto ask_require_nonx_progs
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endif
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else
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set ANS_REQ_NONX=$DEF_REQ_NONX
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endif
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ask_require_x_progs:
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echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
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set ANS_REQ_X = $<
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if ("$ANS_REQ_X" == "?") then
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echo "* These are the programs that require X windows."
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echo " If you do not require all of the X programs, you should abort"
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echo " and manually make the ones you require."
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echo ""
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goto ask_require_x_progs
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else if ("$ANS_REQ_X" != "") then
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if ("$ANS_REQ_X" =~ [yY]*) then
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set ANS_REQ_X=$YES
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else if ("$ANS_REQ_X" =~ [nN]*) then
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set ANS_REQ_X=$NO
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else
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goto ask_require_nonx_progs
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endif
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else
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set ANS_REQ_X=$DEF_REQ_X
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endif
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ask_require_ted:
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echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
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set ANS_REQ_TED = $<
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if ("$ANS_REQ_TED" == "?") then
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echo "* This is the trace editor program. It allows you to look at"
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echo " traces obtained from automated fluorescent sequencing machines."
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echo ""
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goto ask_require_ted
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else if ("$ANS_REQ_TED" != "") then
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if ("$ANS_REQ_TED" =~ [yY]*) then
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set ANS_REQ_TED=$YES
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else if ("$ANS_REQ_TED" =~ [nN]*) then
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set ANS_REQ_TED=$NO
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else
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goto ask_require_ted
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endif
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else
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set ANS_REQ_TED=$DEF_REQ_TED
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endif
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ask_require_misc:
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echo -n "Compile other programs [$DEF_REQ_MISC]? "
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set ANS_REQ_MISC = $<
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if ("$ANS_REQ_MISC" == "?") then
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echo "* Other programs include:"
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echo " alfsplit"
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echo " getABISampleName"
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echo ""
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goto ask_require_misc
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else if ("$ANS_REQ_MISC" != "") then
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if ("$ANS_REQ_MISC" =~ [yY]*) then
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set ANS_REQ_MISC=$YES
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else if ("$ANS_REQ_MISC" =~ [nN]*) then
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set ANS_REQ_MISC=$NO
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else
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goto ask_require_misc
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endif
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else
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set ANS_REQ_MISC=$DEF_REQ_MISC
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endif
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time_taken_warning:
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echo ""
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echo "The installation procedure is now ready to start."
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echo ""
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echo "**** Warning:"
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echo " The installation will take considerable time to complete. If you"
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echo " are installing the whole Staden Package from scratch it could"
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echo " take as long as an hour for all exectuables to be compiled and"
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echo " installed."
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echo ""
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ask_goahead:
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echo -n "Proceed with the installation [YES]? "
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set ANSWER=$<
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if ("$ANSWER" == "?") then
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echo "* Final confirmation to proceed with the installation. Answer"
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echo " YES to proceed; otherwise, answer NO to abort the installation."
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echo ""
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goto ask_goahead
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else if ("$ANSWER" != "") then
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if ("$ANSWER" =~ [nN]*) then
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goto chickens_exit
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else if ("$ANSWER" !~ [yY]*) then
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goto ask_goahead
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endif
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endif
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installation_proper:
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# make binaries directory if it doesn't exist
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if (! -d $DIR_BIN) then
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$MKDIR $DIR_BIN
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endif
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if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
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echo ""
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echo "+ Compiling miscellaneous library"
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pushd $DIR_MISC > /dev/null
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cd $DIR_BINARIES
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$MAKE all
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popd > /dev/null
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endif
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if ("$ANS_REQ_NONX" == "$YES") then
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echo ""
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echo "+ Installing non X programs"
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pushd $DIR_STADEN > /dev/null
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cd $DIR_BINARIES
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$MAKE nprogs lprogs
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$INSTALL mep $DIR_BIN
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$INSTALL nip $DIR_BIN
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$INSTALL pip $DIR_BIN
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$INSTALL sap $DIR_BIN
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$INSTALL sapf $DIR_BIN
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$INSTALL sip $DIR_BIN
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$INSTALL splitp1 $DIR_BIN
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$INSTALL splitp2 $DIR_BIN
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$INSTALL splitp3 $DIR_BIN
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$INSTALL sethelp $DIR_BIN
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$INSTALL gip $DIR_BIN
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$INSTALL nipl $DIR_BIN
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$INSTALL pipl $DIR_BIN
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$INSTALL sipl $DIR_BIN
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$INSTALL dap $DIR_BIN
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$INSTALL nipf $DIR_BIN
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$INSTALL vep $DIR_BIN
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$INSTALL rep $DIR_BIN
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$INSTALL lip $DIR_BIN
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#$INSTALL convert_project $DIR_BIN
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popd > /dev/null
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pushd $DIR_OSP > /dev/null
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cd $DIR_BINARIES
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$MAKE
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popd > /dev/null
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pushd $DIR_BAP > /dev/null
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cd $DIR_BINARIES
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$MAKE bap
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$INSTALL bap $DIR_BIN
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popd > /dev/null
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endif
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if ("$ANS_REQ_TED" == "$YES") then
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echo ""
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echo "+ Installing Trace editor"
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pushd $DIR_TED > /dev/null
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cd $DIR_BINARIES
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$MAKE ted
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$INSTALL ted $DIR_BIN
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popd > /dev/null
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endif
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if ("$ANS_REQ_X" == "$YES") then
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echo ""
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echo "+ Installing X programs"
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pushd $DIR_STADEN > /dev/null
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cd $DIR_BINARIES
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$MAKE xprogs
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$INSTALL xmep $DIR_BIN
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$INSTALL xnip $DIR_BIN
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$INSTALL xpip $DIR_BIN
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$INSTALL xsap $DIR_BIN
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$INSTALL xsip $DIR_BIN
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$INSTALL xdap $DIR_BIN
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popd > /dev/null
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pushd $DIR_OSP > /dev/null
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cd $DIR_BINARIES
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$MAKE
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popd > /dev/null
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pushd $DIR_BAP > /dev/null
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cd $DIR_BINARIES
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$MAKE xbap
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$INSTALL xbap $DIR_BIN
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popd > /dev/null
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endif
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if ("$ANS_REQ_MISC" == "$YES") then
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echo ""
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echo "+ Installing miscellaneous programs"
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pushd $DIR_ABI > /dev/null
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cd $DIR_BINARIES
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$MAKE all
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$INSTALL getABISampleName $DIR_BIN
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popd > /dev/null
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pushd $DIR_ALF > /dev/null
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cd $DIR_BINARIES
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$MAKE alfsplit
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$INSTALL alfsplit $DIR_BIN
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popd > /dev/null
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pushd $DIR_CONVERT > /dev/null
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cd $DIR_BINARIES
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$MAKE convert
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$INSTALL convert $DIR_BIN
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popd > /dev/null
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pushd $DIR_COP > /dev/null
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cd $DIR_BINARIES
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$MAKE all
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$INSTALL cop $DIR_BIN
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$INSTALL cop-bap $DIR_BIN
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popd > /dev/null
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pushd $DIR_FROG > /dev/null
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cd $DIR_BINARIES
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$MAKE frog
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$INSTALL frog $DIR_BIN
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|
|
popd > /dev/null
|
||
|
|
|
||
|
|
pushd $DIR_GETMCH > /dev/null
|
||
|
|
cd $DIR_BINARIES
|
||
|
|
$MAKE trace2seq
|
||
|
|
$INSTALL trace2seq $DIR_BIN
|
||
|
|
popd > /dev/null
|
||
|
|
|
||
|
|
pushd $DIR_SCF > /dev/null
|
||
|
|
cd $DIR_BINARIES
|
||
|
|
$MAKE makeSCF
|
||
|
|
$INSTALL makeSCF $DIR_BIN
|
||
|
|
popd > /dev/null
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
endif
|
||
|
|
|
||
|
|
|
||
|
|
installation_done:
|
||
|
|
echo ""
|
||
|
|
echo "+ Installation completed"
|
||
|
|
echo ""
|
||
|
|
|
||
|
|
echo " Some further initialisation is required in order to use the"
|
||
|
|
echo " package. csh users should insert the following in their .login"
|
||
|
|
echo " files:"
|
||
|
|
echo " "
|
||
|
|
echo " setenv STADENROOT $ANS_STADEN_ROOT"
|
||
|
|
echo ' source $STADENROOT/staden.login'
|
||
|
|
echo " "
|
||
|
|
echo " Users of the Bourne shell, sh, should insert the following in"
|
||
|
|
echo " their .profile:"
|
||
|
|
echo " "
|
||
|
|
echo " STADENROOT=$ANS_STADEN_ROOT"
|
||
|
|
echo " export STADENROOT"
|
||
|
|
echo ' . $STADENROOT/staden.profile'
|
||
|
|
echo " "
|
||
|
|
echo " These initialisations will alter the shell's search path so that"
|
||
|
|
echo " it can find the programs in the STADEN Package"
|
||
|
|
echo " "
|
||
|
|
|
||
|
|
normal_exit:
|
||
|
|
exit 0
|
||
|
|
|
||
|
|
chickens_exit:
|
||
|
|
echo ""
|
||
|
|
echo "+ Installation cancelled"
|
||
|
|
echo ""
|
||
|
|
|
||
|
|
exit 0
|
||
|
|
|
||
|
|
end_failure:
|
||
|
|
unset noglob
|
||
|
|
echo ""
|
||
|
|
echo "Aborted STADEN Package installation on `date`"
|
||
|
|
echo ""
|
||
|
|
exit 1
|
||
|
|
|