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|
@ -0,0 +1,71 @@
|
|||
# STADEN-LG
|
||||
|
||||
STADEN Last Generation
|
||||
|
||||
## Introduction
|
||||
|
||||
<div align="center">
|
||||
<img src="./desktop/staden-lg.png" width = "300" alt="logo" align=center />
|
||||
</div>
|
||||
|
||||
This pkg is a fork of STADEN 1993 v12.1. Currently, I fixed the bug for compiling, but not completely.
|
||||
|
||||
## Build
|
||||
|
||||
You should clone this repo and cd to the repo get the `$pkgname` via `pwd`
|
||||
|
||||
```
|
||||
# build easy
|
||||
for pkgalone in ted newted abi alf Misc cop convert expGetSeq frog getMCH indexseqlibs bap/osp-bits
|
||||
do
|
||||
cd $pkgname/src/$pkgalone
|
||||
make
|
||||
done
|
||||
|
||||
# compile x related
|
||||
cd $pkgname/src/staden
|
||||
bash gen_a.sh
|
||||
make mep dap sap splitp1 splitp2 splitp3 gip sethelp convert_project sapf nipf xmep xdap xsap
|
||||
cd $pkgname/src/bap
|
||||
make bap xbap
|
||||
for pkgalone in vepe update_subclones scf
|
||||
do
|
||||
cd $pkgname/src/$pkgalone
|
||||
make
|
||||
done
|
||||
```
|
||||
|
||||
Or you can get this pkg from BioArchLinux repo.
|
||||
|
||||
## Todo
|
||||
|
||||
Following pkgs need your hands.
|
||||
|
||||
- [ ] nip
|
||||
|
||||
- [ ] sip
|
||||
|
||||
- [ ] rep
|
||||
|
||||
- [ ] lip
|
||||
|
||||
- [ ] vep
|
||||
|
||||
- [ ] nipl
|
||||
|
||||
- [ ] pipl
|
||||
|
||||
- [ ] sipl
|
||||
|
||||
- [ ] xnip
|
||||
|
||||
- [ ] xpip
|
||||
|
||||
- [ ] xsip
|
||||
|
||||
|
||||
## License
|
||||
|
||||
- Copyright (c) 1993 MEDICAL RESEARCH COUNCIL (MRC), UK. BSD License.
|
||||
|
||||
- Copyright (c) 2023~ Everyone. GPL License.
|
|
@ -1,453 +0,0 @@
|
|||
#! /bin/csh -f
|
||||
#
|
||||
# staden_install - version 2.4
|
||||
#
|
||||
# This is a prototype installation program.
|
||||
#
|
||||
# 9 March 1992
|
||||
# Modified for installation on Sun, Alliant, etc
|
||||
# No longer install 2rs
|
||||
#
|
||||
# 20 November 1992
|
||||
# Now includes convert, cop, frog, getMCH and scf
|
||||
#
|
||||
# 25 November 1992
|
||||
# SGI supported
|
||||
#
|
||||
# 19 May 1993
|
||||
# DEC Alpha, Solaris supported
|
||||
#
|
||||
# Written by sd@uk.ac.cam.mrc-lmb
|
||||
#
|
||||
|
||||
# prelim
|
||||
set prog = $0 ; set prog = $prog:t
|
||||
|
||||
# Machines supported: al sun dec sgi alpha solaris
|
||||
#set MACHINE = `echo $prog | sed 's/.*-//'`
|
||||
set MACHINE = alpha
|
||||
|
||||
# For local (MRC-LMB) setup only
|
||||
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
|
||||
set LOCAL = NO
|
||||
|
||||
|
||||
echo ""
|
||||
echo -n "Staden Package installation procedure - "
|
||||
switch (${MACHINE})
|
||||
case "al":
|
||||
echo "Alliant FX/2800 Concentrix version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "sun":
|
||||
echo "SunOS version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "dec":
|
||||
echo "DEC Ultrix (mips) version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "sgi":
|
||||
echo "Silicon Graphics Iris version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "alpha":
|
||||
echo "DEC Alpha OSF/1 version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "solaris":
|
||||
echo "Solaris version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
default:
|
||||
echo "Panic. Unknown version"
|
||||
exit 1
|
||||
endsw
|
||||
echo ""
|
||||
echo "* starting initialization...please wait."
|
||||
echo ""
|
||||
|
||||
# Binary fork of source directory
|
||||
if ($LOCAL == "YES") then
|
||||
set DIR_BINARIES = ${MACHINE}-binaries
|
||||
set DIR_PROGS = ${MACHINE}-bin
|
||||
else
|
||||
set DIR_BINARIES = .
|
||||
set DIR_PROGS = bin
|
||||
set MAKE = "$MAKE -f makefile-${MACHINE}"
|
||||
endif
|
||||
|
||||
init:
|
||||
# Set useful shell variables
|
||||
set YES="YES";
|
||||
set NO="NO"
|
||||
|
||||
# set/unset some .cshrc envs.
|
||||
unset noclobber
|
||||
set noglob
|
||||
|
||||
# set interrupt trap
|
||||
onintr end_failure
|
||||
|
||||
# Make dir command
|
||||
set MKDIR = "mkdir"
|
||||
|
||||
# Copy command
|
||||
set CP = "cp -p"
|
||||
|
||||
# Install command
|
||||
#set INSTALL = "install"
|
||||
#set INSTALL = "mv"
|
||||
set INSTALL = "cp"
|
||||
|
||||
# Set up default responses
|
||||
set DEF_STADEN_ROOT = `pwd`
|
||||
|
||||
set DEF_REQ_NONX = "$YES"
|
||||
set DEF_REQ_X = "$YES"
|
||||
set DEF_REQ_TED = "$YES"
|
||||
set DEF_REQ_MISC = "$YES"
|
||||
|
||||
# directories
|
||||
set DIR_SRC = $DEF_STADEN_ROOT/src
|
||||
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
|
||||
set DIR_MISC = $DIR_SRC/Misc
|
||||
set DIR_STADEN = $DIR_SRC/staden
|
||||
set DIR_TED = $DIR_SRC/ted
|
||||
set DIR_ABI = $DIR_SRC/abi
|
||||
set DIR_ALF = $DIR_SRC/alf
|
||||
set DIR_BAP = $DIR_SRC/bap
|
||||
set DIR_OSP = $DIR_SRC/bap/osp-bits
|
||||
set DIR_CONVERT = $DIR_SRC/convert
|
||||
set DIR_COP = $DIR_SRC/cop
|
||||
set DIR_FROG = $DIR_SRC/frog
|
||||
set DIR_GETMCH = $DIR_SRC/getMCH
|
||||
set DIR_SCF = $DIR_SRC/scf
|
||||
|
||||
|
||||
main:
|
||||
|
||||
|
||||
preamble:
|
||||
echo ""
|
||||
echo ""
|
||||
echo "* Please answer the following questions."
|
||||
echo " Default answers to questions are given in square brackets."
|
||||
echo " If you require help at any stage respond with a ? to the question."
|
||||
echo ""
|
||||
|
||||
ask_staden_root:
|
||||
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
|
||||
|
||||
ask_require_nonx_progs:
|
||||
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
|
||||
set ANS_REQ_NONX = $<
|
||||
if ("$ANS_REQ_NONX" == "?") then
|
||||
echo "* If you do not have X windows on your system you will require"
|
||||
echo " these. However, you will require Tektronics terminal emulation."
|
||||
echo " If you do not require all of the non-X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
echo ""
|
||||
goto ask_require_nonx_progs
|
||||
else if ("$ANS_REQ_NONX" != "") then
|
||||
if ("$ANS_REQ_NONX" =~ [yY]*) then
|
||||
set ANS_REQ_NONX=$YES
|
||||
else if ("$ANS_REQ_NONX" =~ [nN]*) then
|
||||
set ANS_REQ_NONX=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_NONX=$DEF_REQ_NONX
|
||||
endif
|
||||
|
||||
ask_require_x_progs:
|
||||
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
|
||||
set ANS_REQ_X = $<
|
||||
if ("$ANS_REQ_X" == "?") then
|
||||
echo "* These are the programs that require X windows."
|
||||
echo " If you do not require all of the X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
|
||||
echo ""
|
||||
goto ask_require_x_progs
|
||||
else if ("$ANS_REQ_X" != "") then
|
||||
if ("$ANS_REQ_X" =~ [yY]*) then
|
||||
set ANS_REQ_X=$YES
|
||||
else if ("$ANS_REQ_X" =~ [nN]*) then
|
||||
set ANS_REQ_X=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_X=$DEF_REQ_X
|
||||
endif
|
||||
|
||||
|
||||
ask_require_ted:
|
||||
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
|
||||
set ANS_REQ_TED = $<
|
||||
if ("$ANS_REQ_TED" == "?") then
|
||||
echo "* This is the trace editor program. It allows you to look at"
|
||||
echo " traces obtained from automated fluorescent sequencing machines."
|
||||
echo ""
|
||||
goto ask_require_ted
|
||||
else if ("$ANS_REQ_TED" != "") then
|
||||
if ("$ANS_REQ_TED" =~ [yY]*) then
|
||||
set ANS_REQ_TED=$YES
|
||||
else if ("$ANS_REQ_TED" =~ [nN]*) then
|
||||
set ANS_REQ_TED=$NO
|
||||
else
|
||||
goto ask_require_ted
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_TED=$DEF_REQ_TED
|
||||
endif
|
||||
|
||||
|
||||
|
||||
ask_require_misc:
|
||||
echo -n "Compile other programs [$DEF_REQ_MISC]? "
|
||||
set ANS_REQ_MISC = $<
|
||||
if ("$ANS_REQ_MISC" == "?") then
|
||||
echo "* Other programs include:"
|
||||
echo " alfsplit"
|
||||
echo " getABISampleName"
|
||||
echo ""
|
||||
goto ask_require_misc
|
||||
else if ("$ANS_REQ_MISC" != "") then
|
||||
if ("$ANS_REQ_MISC" =~ [yY]*) then
|
||||
set ANS_REQ_MISC=$YES
|
||||
else if ("$ANS_REQ_MISC" =~ [nN]*) then
|
||||
set ANS_REQ_MISC=$NO
|
||||
else
|
||||
goto ask_require_misc
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_MISC=$DEF_REQ_MISC
|
||||
endif
|
||||
|
||||
|
||||
|
||||
time_taken_warning:
|
||||
echo ""
|
||||
echo "The installation procedure is now ready to start."
|
||||
echo ""
|
||||
echo "**** Warning:"
|
||||
echo " The installation will take considerable time to complete. If you"
|
||||
echo " are installing the whole Staden Package from scratch it could"
|
||||
echo " take as long as an hour for all exectuables to be compiled and"
|
||||
echo " installed."
|
||||
echo ""
|
||||
|
||||
ask_goahead:
|
||||
echo -n "Proceed with the installation [YES]? "
|
||||
set ANSWER=$<
|
||||
if ("$ANSWER" == "?") then
|
||||
echo "* Final confirmation to proceed with the installation. Answer"
|
||||
echo " YES to proceed; otherwise, answer NO to abort the installation."
|
||||
echo ""
|
||||
goto ask_goahead
|
||||
else if ("$ANSWER" != "") then
|
||||
if ("$ANSWER" =~ [nN]*) then
|
||||
goto chickens_exit
|
||||
else if ("$ANSWER" !~ [yY]*) then
|
||||
goto ask_goahead
|
||||
endif
|
||||
endif
|
||||
|
||||
installation_proper:
|
||||
|
||||
# make binaries directory if it doesn't exist
|
||||
|
||||
if (! -d $DIR_BIN) then
|
||||
$MKDIR $DIR_BIN
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
|
||||
echo ""
|
||||
echo "+ Compiling miscellaneous library"
|
||||
|
||||
pushd $DIR_MISC > /dev/null
|
||||
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_NONX" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing non X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE nprogs lprogs
|
||||
$INSTALL mep $DIR_BIN
|
||||
$INSTALL nip $DIR_BIN
|
||||
$INSTALL pip $DIR_BIN
|
||||
$INSTALL sap $DIR_BIN
|
||||
$INSTALL sapf $DIR_BIN
|
||||
$INSTALL sip $DIR_BIN
|
||||
$INSTALL splitp1 $DIR_BIN
|
||||
$INSTALL splitp2 $DIR_BIN
|
||||
$INSTALL splitp3 $DIR_BIN
|
||||
$INSTALL sethelp $DIR_BIN
|
||||
$INSTALL gip $DIR_BIN
|
||||
$INSTALL nipl $DIR_BIN
|
||||
$INSTALL pipl $DIR_BIN
|
||||
$INSTALL sipl $DIR_BIN
|
||||
$INSTALL dap $DIR_BIN
|
||||
$INSTALL nipf $DIR_BIN
|
||||
$INSTALL vep $DIR_BIN
|
||||
$INSTALL rep $DIR_BIN
|
||||
$INSTALL lip $DIR_BIN
|
||||
#$INSTALL convert_project $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE bap
|
||||
$INSTALL bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_TED" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing Trace editor"
|
||||
|
||||
pushd $DIR_TED > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE ted
|
||||
$INSTALL ted $DIR_BIN
|
||||
popd > /dev/null
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_X" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xprogs
|
||||
$INSTALL xmep $DIR_BIN
|
||||
$INSTALL xnip $DIR_BIN
|
||||
$INSTALL xpip $DIR_BIN
|
||||
$INSTALL xsap $DIR_BIN
|
||||
$INSTALL xsip $DIR_BIN
|
||||
$INSTALL xdap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xbap
|
||||
$INSTALL xbap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing miscellaneous programs"
|
||||
|
||||
pushd $DIR_ABI > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL getABISampleName $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_ALF > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE alfsplit
|
||||
$INSTALL alfsplit $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_CONVERT > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE convert
|
||||
$INSTALL convert $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_COP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL cop $DIR_BIN
|
||||
$INSTALL cop-bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_FROG > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE frog
|
||||
$INSTALL frog $DIR_BIN
|
||||
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
|
||||
|
|
@ -1,453 +0,0 @@
|
|||
#! /bin/csh -f
|
||||
#
|
||||
# staden_install - version 2.4
|
||||
#
|
||||
# This is a prototype installation program.
|
||||
#
|
||||
# 9 March 1992
|
||||
# Modified for installation on Sun, Alliant, etc
|
||||
# No longer install 2rs
|
||||
#
|
||||
# 20 November 1992
|
||||
# Now includes convert, cop, frog, getMCH and scf
|
||||
#
|
||||
# 25 November 1992
|
||||
# SGI supported
|
||||
#
|
||||
# 19 May 1993
|
||||
# DEC Alpha, Solaris supported
|
||||
#
|
||||
# Written by sd@uk.ac.cam.mrc-lmb
|
||||
#
|
||||
|
||||
# prelim
|
||||
set prog = $0 ; set prog = $prog:t
|
||||
|
||||
# Machines supported: al sun dec sgi alpha solaris
|
||||
#set MACHINE = `echo $prog | sed 's/.*-//'`
|
||||
set MACHINE = dec
|
||||
|
||||
# For local (MRC-LMB) setup only
|
||||
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
|
||||
set LOCAL = NO
|
||||
|
||||
|
||||
echo ""
|
||||
echo -n "Staden Package installation procedure - "
|
||||
switch (${MACHINE})
|
||||
case "al":
|
||||
echo "Alliant FX/2800 Concentrix version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "sun":
|
||||
echo "SunOS version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "dec":
|
||||
echo "DEC Ultrix (mips) version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "sgi":
|
||||
echo "Silicon Graphics Iris version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "alpha":
|
||||
echo "DEC Alpha OSF/1 version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "solaris":
|
||||
echo "Solaris version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
default:
|
||||
echo "Panic. Unknown version"
|
||||
exit 1
|
||||
endsw
|
||||
echo ""
|
||||
echo "* starting initialization...please wait."
|
||||
echo ""
|
||||
|
||||
# Binary fork of source directory
|
||||
if ($LOCAL == "YES") then
|
||||
set DIR_BINARIES = ${MACHINE}-binaries
|
||||
set DIR_PROGS = ${MACHINE}-bin
|
||||
else
|
||||
set DIR_BINARIES = .
|
||||
set DIR_PROGS = bin
|
||||
set MAKE = "$MAKE -f makefile-${MACHINE}"
|
||||
endif
|
||||
|
||||
init:
|
||||
# Set useful shell variables
|
||||
set YES="YES";
|
||||
set NO="NO"
|
||||
|
||||
# set/unset some .cshrc envs.
|
||||
unset noclobber
|
||||
set noglob
|
||||
|
||||
# set interrupt trap
|
||||
onintr end_failure
|
||||
|
||||
# Make dir command
|
||||
set MKDIR = "mkdir"
|
||||
|
||||
# Copy command
|
||||
set CP = "cp -p"
|
||||
|
||||
# Install command
|
||||
#set INSTALL = "install"
|
||||
#set INSTALL = "mv"
|
||||
set INSTALL = "cp"
|
||||
|
||||
# Set up default responses
|
||||
set DEF_STADEN_ROOT = `pwd`
|
||||
|
||||
set DEF_REQ_NONX = "$YES"
|
||||
set DEF_REQ_X = "$YES"
|
||||
set DEF_REQ_TED = "$YES"
|
||||
set DEF_REQ_MISC = "$YES"
|
||||
|
||||
# directories
|
||||
set DIR_SRC = $DEF_STADEN_ROOT/src
|
||||
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
|
||||
set DIR_MISC = $DIR_SRC/Misc
|
||||
set DIR_STADEN = $DIR_SRC/staden
|
||||
set DIR_TED = $DIR_SRC/ted
|
||||
set DIR_ABI = $DIR_SRC/abi
|
||||
set DIR_ALF = $DIR_SRC/alf
|
||||
set DIR_BAP = $DIR_SRC/bap
|
||||
set DIR_OSP = $DIR_SRC/bap/osp-bits
|
||||
set DIR_CONVERT = $DIR_SRC/convert
|
||||
set DIR_COP = $DIR_SRC/cop
|
||||
set DIR_FROG = $DIR_SRC/frog
|
||||
set DIR_GETMCH = $DIR_SRC/getMCH
|
||||
set DIR_SCF = $DIR_SRC/scf
|
||||
|
||||
|
||||
main:
|
||||
|
||||
|
||||
preamble:
|
||||
echo ""
|
||||
echo ""
|
||||
echo "* Please answer the following questions."
|
||||
echo " Default answers to questions are given in square brackets."
|
||||
echo " If you require help at any stage respond with a ? to the question."
|
||||
echo ""
|
||||
|
||||
ask_staden_root:
|
||||
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
|
||||
|
||||
ask_require_nonx_progs:
|
||||
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
|
||||
set ANS_REQ_NONX = $<
|
||||
if ("$ANS_REQ_NONX" == "?") then
|
||||
echo "* If you do not have X windows on your system you will require"
|
||||
echo " these. However, you will require Tektronics terminal emulation."
|
||||
echo " If you do not require all of the non-X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
echo ""
|
||||
goto ask_require_nonx_progs
|
||||
else if ("$ANS_REQ_NONX" != "") then
|
||||
if ("$ANS_REQ_NONX" =~ [yY]*) then
|
||||
set ANS_REQ_NONX=$YES
|
||||
else if ("$ANS_REQ_NONX" =~ [nN]*) then
|
||||
set ANS_REQ_NONX=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_NONX=$DEF_REQ_NONX
|
||||
endif
|
||||
|
||||
ask_require_x_progs:
|
||||
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
|
||||
set ANS_REQ_X = $<
|
||||
if ("$ANS_REQ_X" == "?") then
|
||||
echo "* These are the programs that require X windows."
|
||||
echo " If you do not require all of the X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
|
||||
echo ""
|
||||
goto ask_require_x_progs
|
||||
else if ("$ANS_REQ_X" != "") then
|
||||
if ("$ANS_REQ_X" =~ [yY]*) then
|
||||
set ANS_REQ_X=$YES
|
||||
else if ("$ANS_REQ_X" =~ [nN]*) then
|
||||
set ANS_REQ_X=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_X=$DEF_REQ_X
|
||||
endif
|
||||
|
||||
|
||||
ask_require_ted:
|
||||
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
|
||||
set ANS_REQ_TED = $<
|
||||
if ("$ANS_REQ_TED" == "?") then
|
||||
echo "* This is the trace editor program. It allows you to look at"
|
||||
echo " traces obtained from automated fluorescent sequencing machines."
|
||||
echo ""
|
||||
goto ask_require_ted
|
||||
else if ("$ANS_REQ_TED" != "") then
|
||||
if ("$ANS_REQ_TED" =~ [yY]*) then
|
||||
set ANS_REQ_TED=$YES
|
||||
else if ("$ANS_REQ_TED" =~ [nN]*) then
|
||||
set ANS_REQ_TED=$NO
|
||||
else
|
||||
goto ask_require_ted
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_TED=$DEF_REQ_TED
|
||||
endif
|
||||
|
||||
|
||||
|
||||
ask_require_misc:
|
||||
echo -n "Compile other programs [$DEF_REQ_MISC]? "
|
||||
set ANS_REQ_MISC = $<
|
||||
if ("$ANS_REQ_MISC" == "?") then
|
||||
echo "* Other programs include:"
|
||||
echo " alfsplit"
|
||||
echo " getABISampleName"
|
||||
echo ""
|
||||
goto ask_require_misc
|
||||
else if ("$ANS_REQ_MISC" != "") then
|
||||
if ("$ANS_REQ_MISC" =~ [yY]*) then
|
||||
set ANS_REQ_MISC=$YES
|
||||
else if ("$ANS_REQ_MISC" =~ [nN]*) then
|
||||
set ANS_REQ_MISC=$NO
|
||||
else
|
||||
goto ask_require_misc
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_MISC=$DEF_REQ_MISC
|
||||
endif
|
||||
|
||||
|
||||
|
||||
time_taken_warning:
|
||||
echo ""
|
||||
echo "The installation procedure is now ready to start."
|
||||
echo ""
|
||||
echo "**** Warning:"
|
||||
echo " The installation will take considerable time to complete. If you"
|
||||
echo " are installing the whole Staden Package from scratch it could"
|
||||
echo " take as long as an hour for all exectuables to be compiled and"
|
||||
echo " installed."
|
||||
echo ""
|
||||
|
||||
ask_goahead:
|
||||
echo -n "Proceed with the installation [YES]? "
|
||||
set ANSWER=$<
|
||||
if ("$ANSWER" == "?") then
|
||||
echo "* Final confirmation to proceed with the installation. Answer"
|
||||
echo " YES to proceed; otherwise, answer NO to abort the installation."
|
||||
echo ""
|
||||
goto ask_goahead
|
||||
else if ("$ANSWER" != "") then
|
||||
if ("$ANSWER" =~ [nN]*) then
|
||||
goto chickens_exit
|
||||
else if ("$ANSWER" !~ [yY]*) then
|
||||
goto ask_goahead
|
||||
endif
|
||||
endif
|
||||
|
||||
installation_proper:
|
||||
|
||||
# make binaries directory if it doesn't exist
|
||||
|
||||
if (! -d $DIR_BIN) then
|
||||
$MKDIR $DIR_BIN
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
|
||||
echo ""
|
||||
echo "+ Compiling miscellaneous library"
|
||||
|
||||
pushd $DIR_MISC > /dev/null
|
||||
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_NONX" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing non X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE nprogs lprogs
|
||||
$INSTALL mep $DIR_BIN
|
||||
$INSTALL nip $DIR_BIN
|
||||
$INSTALL pip $DIR_BIN
|
||||
$INSTALL sap $DIR_BIN
|
||||
$INSTALL sapf $DIR_BIN
|
||||
$INSTALL sip $DIR_BIN
|
||||
$INSTALL splitp1 $DIR_BIN
|
||||
$INSTALL splitp2 $DIR_BIN
|
||||
$INSTALL splitp3 $DIR_BIN
|
||||
$INSTALL sethelp $DIR_BIN
|
||||
$INSTALL gip $DIR_BIN
|
||||
$INSTALL nipl $DIR_BIN
|
||||
$INSTALL pipl $DIR_BIN
|
||||
$INSTALL sipl $DIR_BIN
|
||||
$INSTALL dap $DIR_BIN
|
||||
$INSTALL nipf $DIR_BIN
|
||||
$INSTALL vep $DIR_BIN
|
||||
$INSTALL rep $DIR_BIN
|
||||
$INSTALL lip $DIR_BIN
|
||||
#$INSTALL convert_project $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE bap
|
||||
$INSTALL bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_TED" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing Trace editor"
|
||||
|
||||
pushd $DIR_TED > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE ted
|
||||
$INSTALL ted $DIR_BIN
|
||||
popd > /dev/null
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_X" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xprogs
|
||||
$INSTALL xmep $DIR_BIN
|
||||
$INSTALL xnip $DIR_BIN
|
||||
$INSTALL xpip $DIR_BIN
|
||||
$INSTALL xsap $DIR_BIN
|
||||
$INSTALL xsip $DIR_BIN
|
||||
$INSTALL xdap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xbap
|
||||
$INSTALL xbap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing miscellaneous programs"
|
||||
|
||||
pushd $DIR_ABI > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL getABISampleName $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_ALF > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE alfsplit
|
||||
$INSTALL alfsplit $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_CONVERT > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE convert
|
||||
$INSTALL convert $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_COP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL cop $DIR_BIN
|
||||
$INSTALL cop-bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_FROG > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE frog
|
||||
$INSTALL frog $DIR_BIN
|
||||
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
|
||||
|
|
@ -1,453 +0,0 @@
|
|||
#! /bin/csh -f
|
||||
#
|
||||
# staden_install - version 2.4
|
||||
#
|
||||
# This is a prototype installation program.
|
||||
#
|
||||
# 9 March 1992
|
||||
# Modified for installation on Sun, Alliant, etc
|
||||
# No longer install 2rs
|
||||
#
|
||||
# 20 November 1992
|
||||
# Now includes convert, cop, frog, getMCH and scf
|
||||
#
|
||||
# 25 November 1992
|
||||
# SGI supported
|
||||
#
|
||||
# 19 May 1993
|
||||
# DEC Alpha, Solaris supported
|
||||
#
|
||||
# Written by sd@uk.ac.cam.mrc-lmb
|
||||
#
|
||||
|
||||
# prelim
|
||||
set prog = $0 ; set prog = $prog:t
|
||||
|
||||
# Machines supported: al sun dec sgi alpha solaris
|
||||
#set MACHINE = `echo $prog | sed 's/.*-//'`
|
||||
set MACHINE = sgi
|
||||
|
||||
# For local (MRC-LMB) setup only
|
||||
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
|
||||
set LOCAL = NO
|
||||
|
||||
|
||||
echo ""
|
||||
echo -n "Staden Package installation procedure - "
|
||||
switch (${MACHINE})
|
||||
case "al":
|
||||
echo "Alliant FX/2800 Concentrix version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "sun":
|
||||
echo "SunOS version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "dec":
|
||||
echo "DEC Ultrix (mips) version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "sgi":
|
||||
echo "Silicon Graphics Iris version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "alpha":
|
||||
echo "DEC Alpha OSF/1 version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "solaris":
|
||||
echo "Solaris version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
default:
|
||||
echo "Panic. Unknown version"
|
||||
exit 1
|
||||
endsw
|
||||
echo ""
|
||||
echo "* starting initialization...please wait."
|
||||
echo ""
|
||||
|
||||
# Binary fork of source directory
|
||||
if ($LOCAL == "YES") then
|
||||
set DIR_BINARIES = ${MACHINE}-binaries
|
||||
set DIR_PROGS = ${MACHINE}-bin
|
||||
else
|
||||
set DIR_BINARIES = .
|
||||
set DIR_PROGS = bin
|
||||
set MAKE = "$MAKE -f makefile-${MACHINE}"
|
||||
endif
|
||||
|
||||
init:
|
||||
# Set useful shell variables
|
||||
set YES="YES";
|
||||
set NO="NO"
|
||||
|
||||
# set/unset some .cshrc envs.
|
||||
unset noclobber
|
||||
set noglob
|
||||
|
||||
# set interrupt trap
|
||||
onintr end_failure
|
||||
|
||||
# Make dir command
|
||||
set MKDIR = "mkdir"
|
||||
|
||||
# Copy command
|
||||
set CP = "cp -p"
|
||||
|
||||
# Install command
|
||||
#set INSTALL = "install"
|
||||
#set INSTALL = "mv"
|
||||
set INSTALL = "cp"
|
||||
|
||||
# Set up default responses
|
||||
set DEF_STADEN_ROOT = `pwd`
|
||||
|
||||
set DEF_REQ_NONX = "$YES"
|
||||
set DEF_REQ_X = "$YES"
|
||||
set DEF_REQ_TED = "$YES"
|
||||
set DEF_REQ_MISC = "$YES"
|
||||
|
||||
# directories
|
||||
set DIR_SRC = $DEF_STADEN_ROOT/src
|
||||
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
|
||||
set DIR_MISC = $DIR_SRC/Misc
|
||||
set DIR_STADEN = $DIR_SRC/staden
|
||||
set DIR_TED = $DIR_SRC/ted
|
||||
set DIR_ABI = $DIR_SRC/abi
|
||||
set DIR_ALF = $DIR_SRC/alf
|
||||
set DIR_BAP = $DIR_SRC/bap
|
||||
set DIR_OSP = $DIR_SRC/bap/osp-bits
|
||||
set DIR_CONVERT = $DIR_SRC/convert
|
||||
set DIR_COP = $DIR_SRC/cop
|
||||
set DIR_FROG = $DIR_SRC/frog
|
||||
set DIR_GETMCH = $DIR_SRC/getMCH
|
||||
set DIR_SCF = $DIR_SRC/scf
|
||||
|
||||
|
||||
main:
|
||||
|
||||
|
||||
preamble:
|
||||
echo ""
|
||||
echo ""
|
||||
echo "* Please answer the following questions."
|
||||
echo " Default answers to questions are given in square brackets."
|
||||
echo " If you require help at any stage respond with a ? to the question."
|
||||
echo ""
|
||||
|
||||
ask_staden_root:
|
||||
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
|
||||
|
||||
ask_require_nonx_progs:
|
||||
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
|
||||
set ANS_REQ_NONX = $<
|
||||
if ("$ANS_REQ_NONX" == "?") then
|
||||
echo "* If you do not have X windows on your system you will require"
|
||||
echo " these. However, you will require Tektronics terminal emulation."
|
||||
echo " If you do not require all of the non-X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
echo ""
|
||||
goto ask_require_nonx_progs
|
||||
else if ("$ANS_REQ_NONX" != "") then
|
||||
if ("$ANS_REQ_NONX" =~ [yY]*) then
|
||||
set ANS_REQ_NONX=$YES
|
||||
else if ("$ANS_REQ_NONX" =~ [nN]*) then
|
||||
set ANS_REQ_NONX=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_NONX=$DEF_REQ_NONX
|
||||
endif
|
||||
|
||||
ask_require_x_progs:
|
||||
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
|
||||
set ANS_REQ_X = $<
|
||||
if ("$ANS_REQ_X" == "?") then
|
||||
echo "* These are the programs that require X windows."
|
||||
echo " If you do not require all of the X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
|
||||
echo ""
|
||||
goto ask_require_x_progs
|
||||
else if ("$ANS_REQ_X" != "") then
|
||||
if ("$ANS_REQ_X" =~ [yY]*) then
|
||||
set ANS_REQ_X=$YES
|
||||
else if ("$ANS_REQ_X" =~ [nN]*) then
|
||||
set ANS_REQ_X=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_X=$DEF_REQ_X
|
||||
endif
|
||||
|
||||
|
||||
ask_require_ted:
|
||||
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
|
||||
set ANS_REQ_TED = $<
|
||||
if ("$ANS_REQ_TED" == "?") then
|
||||
echo "* This is the trace editor program. It allows you to look at"
|
||||
echo " traces obtained from automated fluorescent sequencing machines."
|
||||
echo ""
|
||||
goto ask_require_ted
|
||||
else if ("$ANS_REQ_TED" != "") then
|
||||
if ("$ANS_REQ_TED" =~ [yY]*) then
|
||||
set ANS_REQ_TED=$YES
|
||||
else if ("$ANS_REQ_TED" =~ [nN]*) then
|
||||
set ANS_REQ_TED=$NO
|
||||
else
|
||||
goto ask_require_ted
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_TED=$DEF_REQ_TED
|
||||
endif
|
||||
|
||||
|
||||
|
||||
ask_require_misc:
|
||||
echo -n "Compile other programs [$DEF_REQ_MISC]? "
|
||||
set ANS_REQ_MISC = $<
|
||||
if ("$ANS_REQ_MISC" == "?") then
|
||||
echo "* Other programs include:"
|
||||
echo " alfsplit"
|
||||
echo " getABISampleName"
|
||||
echo ""
|
||||
goto ask_require_misc
|
||||
else if ("$ANS_REQ_MISC" != "") then
|
||||
if ("$ANS_REQ_MISC" =~ [yY]*) then
|
||||
set ANS_REQ_MISC=$YES
|
||||
else if ("$ANS_REQ_MISC" =~ [nN]*) then
|
||||
set ANS_REQ_MISC=$NO
|
||||
else
|
||||
goto ask_require_misc
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_MISC=$DEF_REQ_MISC
|
||||
endif
|
||||
|
||||
|
||||
|
||||
time_taken_warning:
|
||||
echo ""
|
||||
echo "The installation procedure is now ready to start."
|
||||
echo ""
|
||||
echo "**** Warning:"
|
||||
echo " The installation will take considerable time to complete. If you"
|
||||
echo " are installing the whole Staden Package from scratch it could"
|
||||
echo " take as long as an hour for all exectuables to be compiled and"
|
||||
echo " installed."
|
||||
echo ""
|
||||
|
||||
ask_goahead:
|
||||
echo -n "Proceed with the installation [YES]? "
|
||||
set ANSWER=$<
|
||||
if ("$ANSWER" == "?") then
|
||||
echo "* Final confirmation to proceed with the installation. Answer"
|
||||
echo " YES to proceed; otherwise, answer NO to abort the installation."
|
||||
echo ""
|
||||
goto ask_goahead
|
||||
else if ("$ANSWER" != "") then
|
||||
if ("$ANSWER" =~ [nN]*) then
|
||||
goto chickens_exit
|
||||
else if ("$ANSWER" !~ [yY]*) then
|
||||
goto ask_goahead
|
||||
endif
|
||||
endif
|
||||
|
||||
installation_proper:
|
||||
|
||||
# make binaries directory if it doesn't exist
|
||||
|
||||
if (! -d $DIR_BIN) then
|
||||
$MKDIR $DIR_BIN
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
|
||||
echo ""
|
||||
echo "+ Compiling miscellaneous library"
|
||||
|
||||
pushd $DIR_MISC > /dev/null
|
||||
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_NONX" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing non X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE nprogs lprogs
|
||||
$INSTALL mep $DIR_BIN
|
||||
$INSTALL nip $DIR_BIN
|
||||
$INSTALL pip $DIR_BIN
|
||||
$INSTALL sap $DIR_BIN
|
||||
$INSTALL sapf $DIR_BIN
|
||||
$INSTALL sip $DIR_BIN
|
||||
$INSTALL splitp1 $DIR_BIN
|
||||
$INSTALL splitp2 $DIR_BIN
|
||||
$INSTALL splitp3 $DIR_BIN
|
||||
$INSTALL sethelp $DIR_BIN
|
||||
$INSTALL gip $DIR_BIN
|
||||
$INSTALL nipl $DIR_BIN
|
||||
$INSTALL pipl $DIR_BIN
|
||||
$INSTALL sipl $DIR_BIN
|
||||
$INSTALL dap $DIR_BIN
|
||||
$INSTALL nipf $DIR_BIN
|
||||
$INSTALL vep $DIR_BIN
|
||||
$INSTALL rep $DIR_BIN
|
||||
$INSTALL lip $DIR_BIN
|
||||
#$INSTALL convert_project $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE bap
|
||||
$INSTALL bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_TED" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing Trace editor"
|
||||
|
||||
pushd $DIR_TED > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE ted
|
||||
$INSTALL ted $DIR_BIN
|
||||
popd > /dev/null
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_X" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xprogs
|
||||
$INSTALL xmep $DIR_BIN
|
||||
$INSTALL xnip $DIR_BIN
|
||||
$INSTALL xpip $DIR_BIN
|
||||
$INSTALL xsap $DIR_BIN
|
||||
$INSTALL xsip $DIR_BIN
|
||||
$INSTALL xdap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xbap
|
||||
$INSTALL xbap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing miscellaneous programs"
|
||||
|
||||
pushd $DIR_ABI > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL getABISampleName $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_ALF > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE alfsplit
|
||||
$INSTALL alfsplit $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_CONVERT > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE convert
|
||||
$INSTALL convert $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_COP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL cop $DIR_BIN
|
||||
$INSTALL cop-bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_FROG > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE frog
|
||||
$INSTALL frog $DIR_BIN
|
||||
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
|
||||
|
|
@ -1,453 +0,0 @@
|
|||
#! /bin/csh -f
|
||||
#
|
||||
# staden_install - version 2.4
|
||||
#
|
||||
# This is a prototype installation program.
|
||||
#
|
||||
# 9 March 1992
|
||||
# Modified for installation on Sun, Alliant, etc
|
||||
# No longer install 2rs
|
||||
#
|
||||
# 20 November 1992
|
||||
# Now includes convert, cop, frog, getMCH and scf
|
||||
#
|
||||
# 25 November 1992
|
||||
# SGI supported
|
||||
#
|
||||
# 19 May 1993
|
||||
# DEC Alpha, Solaris supported
|
||||
#
|
||||
# Written by sd@uk.ac.cam.mrc-lmb
|
||||
#
|
||||
|
||||
# prelim
|
||||
set prog = $0 ; set prog = $prog:t
|
||||
|
||||
# Machines supported: al sun dec sgi alpha solaris
|
||||
#set MACHINE = `echo $prog | sed 's/.*-//'`
|
||||
set MACHINE = solaris
|
||||
|
||||
# For local (MRC-LMB) setup only
|
||||
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
|
||||
set LOCAL = NO
|
||||
|
||||
|
||||
echo ""
|
||||
echo -n "Staden Package installation procedure - "
|
||||
switch (${MACHINE})
|
||||
case "al":
|
||||
echo "Alliant FX/2800 Concentrix version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "sun":
|
||||
echo "SunOS version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "dec":
|
||||
echo "DEC Ultrix (mips) version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "sgi":
|
||||
echo "Silicon Graphics Iris version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "alpha":
|
||||
echo "DEC Alpha OSF/1 version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "solaris":
|
||||
echo "Solaris version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
default:
|
||||
echo "Panic. Unknown version"
|
||||
exit 1
|
||||
endsw
|
||||
echo ""
|
||||
echo "* starting initialization...please wait."
|
||||
echo ""
|
||||
|
||||
# Binary fork of source directory
|
||||
if ($LOCAL == "YES") then
|
||||
set DIR_BINARIES = ${MACHINE}-binaries
|
||||
set DIR_PROGS = ${MACHINE}-bin
|
||||
else
|
||||
set DIR_BINARIES = .
|
||||
set DIR_PROGS = bin
|
||||
set MAKE = "$MAKE -f makefile-${MACHINE}"
|
||||
endif
|
||||
|
||||
init:
|
||||
# Set useful shell variables
|
||||
set YES="YES";
|
||||
set NO="NO"
|
||||
|
||||
# set/unset some .cshrc envs.
|
||||
unset noclobber
|
||||
set noglob
|
||||
|
||||
# set interrupt trap
|
||||
onintr end_failure
|
||||
|
||||
# Make dir command
|
||||
set MKDIR = "mkdir"
|
||||
|
||||
# Copy command
|
||||
set CP = "cp -p"
|
||||
|
||||
# Install command
|
||||
#set INSTALL = "install"
|
||||
#set INSTALL = "mv"
|
||||
set INSTALL = "cp"
|
||||
|
||||
# Set up default responses
|
||||
set DEF_STADEN_ROOT = `pwd`
|
||||
|
||||
set DEF_REQ_NONX = "$YES"
|
||||
set DEF_REQ_X = "$YES"
|
||||
set DEF_REQ_TED = "$YES"
|
||||
set DEF_REQ_MISC = "$YES"
|
||||
|
||||
# directories
|
||||
set DIR_SRC = $DEF_STADEN_ROOT/src
|
||||
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
|
||||
set DIR_MISC = $DIR_SRC/Misc
|
||||
set DIR_STADEN = $DIR_SRC/staden
|
||||
set DIR_TED = $DIR_SRC/ted
|
||||
set DIR_ABI = $DIR_SRC/abi
|
||||
set DIR_ALF = $DIR_SRC/alf
|
||||
set DIR_BAP = $DIR_SRC/bap
|
||||
set DIR_OSP = $DIR_SRC/bap/osp-bits
|
||||
set DIR_CONVERT = $DIR_SRC/convert
|
||||
set DIR_COP = $DIR_SRC/cop
|
||||
set DIR_FROG = $DIR_SRC/frog
|
||||
set DIR_GETMCH = $DIR_SRC/getMCH
|
||||
set DIR_SCF = $DIR_SRC/scf
|
||||
|
||||
|
||||
main:
|
||||
|
||||
|
||||
preamble:
|
||||
echo ""
|
||||
echo ""
|
||||
echo "* Please answer the following questions."
|
||||
echo " Default answers to questions are given in square brackets."
|
||||
echo " If you require help at any stage respond with a ? to the question."
|
||||
echo ""
|
||||
|
||||
ask_staden_root:
|
||||
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
|
||||
|
||||
ask_require_nonx_progs:
|
||||
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
|
||||
set ANS_REQ_NONX = $<
|
||||
if ("$ANS_REQ_NONX" == "?") then
|
||||
echo "* If you do not have X windows on your system you will require"
|
||||
echo " these. However, you will require Tektronics terminal emulation."
|
||||
echo " If you do not require all of the non-X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
echo ""
|
||||
goto ask_require_nonx_progs
|
||||
else if ("$ANS_REQ_NONX" != "") then
|
||||
if ("$ANS_REQ_NONX" =~ [yY]*) then
|
||||
set ANS_REQ_NONX=$YES
|
||||
else if ("$ANS_REQ_NONX" =~ [nN]*) then
|
||||
set ANS_REQ_NONX=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_NONX=$DEF_REQ_NONX
|
||||
endif
|
||||
|
||||
ask_require_x_progs:
|
||||
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
|
||||
set ANS_REQ_X = $<
|
||||
if ("$ANS_REQ_X" == "?") then
|
||||
echo "* These are the programs that require X windows."
|
||||
echo " If you do not require all of the X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
|
||||
echo ""
|
||||
goto ask_require_x_progs
|
||||
else if ("$ANS_REQ_X" != "") then
|
||||
if ("$ANS_REQ_X" =~ [yY]*) then
|
||||
set ANS_REQ_X=$YES
|
||||
else if ("$ANS_REQ_X" =~ [nN]*) then
|
||||
set ANS_REQ_X=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_X=$DEF_REQ_X
|
||||
endif
|
||||
|
||||
|
||||
ask_require_ted:
|
||||
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
|
||||
set ANS_REQ_TED = $<
|
||||
if ("$ANS_REQ_TED" == "?") then
|
||||
echo "* This is the trace editor program. It allows you to look at"
|
||||
echo " traces obtained from automated fluorescent sequencing machines."
|
||||
echo ""
|
||||
goto ask_require_ted
|
||||
else if ("$ANS_REQ_TED" != "") then
|
||||
if ("$ANS_REQ_TED" =~ [yY]*) then
|
||||
set ANS_REQ_TED=$YES
|
||||
else if ("$ANS_REQ_TED" =~ [nN]*) then
|
||||
set ANS_REQ_TED=$NO
|
||||
else
|
||||
goto ask_require_ted
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_TED=$DEF_REQ_TED
|
||||
endif
|
||||
|
||||
|
||||
|
||||
ask_require_misc:
|
||||
echo -n "Compile other programs [$DEF_REQ_MISC]? "
|
||||
set ANS_REQ_MISC = $<
|
||||
if ("$ANS_REQ_MISC" == "?") then
|
||||
echo "* Other programs include:"
|
||||
echo " alfsplit"
|
||||
echo " getABISampleName"
|
||||
echo ""
|
||||
goto ask_require_misc
|
||||
else if ("$ANS_REQ_MISC" != "") then
|
||||
if ("$ANS_REQ_MISC" =~ [yY]*) then
|
||||
set ANS_REQ_MISC=$YES
|
||||
else if ("$ANS_REQ_MISC" =~ [nN]*) then
|
||||
set ANS_REQ_MISC=$NO
|
||||
else
|
||||
goto ask_require_misc
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_MISC=$DEF_REQ_MISC
|
||||
endif
|
||||
|
||||
|
||||
|
||||
time_taken_warning:
|
||||
echo ""
|
||||
echo "The installation procedure is now ready to start."
|
||||
echo ""
|
||||
echo "**** Warning:"
|
||||
echo " The installation will take considerable time to complete. If you"
|
||||
echo " are installing the whole Staden Package from scratch it could"
|
||||
echo " take as long as an hour for all exectuables to be compiled and"
|
||||
echo " installed."
|
||||
echo ""
|
||||
|
||||
ask_goahead:
|
||||
echo -n "Proceed with the installation [YES]? "
|
||||
set ANSWER=$<
|
||||
if ("$ANSWER" == "?") then
|
||||
echo "* Final confirmation to proceed with the installation. Answer"
|
||||
echo " YES to proceed; otherwise, answer NO to abort the installation."
|
||||
echo ""
|
||||
goto ask_goahead
|
||||
else if ("$ANSWER" != "") then
|
||||
if ("$ANSWER" =~ [nN]*) then
|
||||
goto chickens_exit
|
||||
else if ("$ANSWER" !~ [yY]*) then
|
||||
goto ask_goahead
|
||||
endif
|
||||
endif
|
||||
|
||||
installation_proper:
|
||||
|
||||
# make binaries directory if it doesn't exist
|
||||
|
||||
if (! -d $DIR_BIN) then
|
||||
$MKDIR $DIR_BIN
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
|
||||
echo ""
|
||||
echo "+ Compiling miscellaneous library"
|
||||
|
||||
pushd $DIR_MISC > /dev/null
|
||||
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_NONX" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing non X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE nprogs lprogs
|
||||
$INSTALL mep $DIR_BIN
|
||||
$INSTALL nip $DIR_BIN
|
||||
$INSTALL pip $DIR_BIN
|
||||
$INSTALL sap $DIR_BIN
|
||||
$INSTALL sapf $DIR_BIN
|
||||
$INSTALL sip $DIR_BIN
|
||||
$INSTALL splitp1 $DIR_BIN
|
||||
$INSTALL splitp2 $DIR_BIN
|
||||
$INSTALL splitp3 $DIR_BIN
|
||||
$INSTALL sethelp $DIR_BIN
|
||||
$INSTALL gip $DIR_BIN
|
||||
$INSTALL nipl $DIR_BIN
|
||||
$INSTALL pipl $DIR_BIN
|
||||
$INSTALL sipl $DIR_BIN
|
||||
$INSTALL dap $DIR_BIN
|
||||
$INSTALL nipf $DIR_BIN
|
||||
$INSTALL vep $DIR_BIN
|
||||
$INSTALL rep $DIR_BIN
|
||||
$INSTALL lip $DIR_BIN
|
||||
#$INSTALL convert_project $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE bap
|
||||
$INSTALL bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_TED" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing Trace editor"
|
||||
|
||||
pushd $DIR_TED > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE ted
|
||||
$INSTALL ted $DIR_BIN
|
||||
popd > /dev/null
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_X" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xprogs
|
||||
$INSTALL xmep $DIR_BIN
|
||||
$INSTALL xnip $DIR_BIN
|
||||
$INSTALL xpip $DIR_BIN
|
||||
$INSTALL xsap $DIR_BIN
|
||||
$INSTALL xsip $DIR_BIN
|
||||
$INSTALL xdap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xbap
|
||||
$INSTALL xbap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing miscellaneous programs"
|
||||
|
||||
pushd $DIR_ABI > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL getABISampleName $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_ALF > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE alfsplit
|
||||
$INSTALL alfsplit $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_CONVERT > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE convert
|
||||
$INSTALL convert $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_COP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL cop $DIR_BIN
|
||||
$INSTALL cop-bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_FROG > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE frog
|
||||
$INSTALL frog $DIR_BIN
|
||||
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
|
||||
|
|
@ -1,453 +0,0 @@
|
|||
#! /bin/csh -f
|
||||
#
|
||||
# staden_install - version 2.4
|
||||
#
|
||||
# This is a prototype installation program.
|
||||
#
|
||||
# 9 March 1992
|
||||
# Modified for installation on Sun, Alliant, etc
|
||||
# No longer install 2rs
|
||||
#
|
||||
# 20 November 1992
|
||||
# Now includes convert, cop, frog, getMCH and scf
|
||||
#
|
||||
# 25 November 1992
|
||||
# SGI supported
|
||||
#
|
||||
# 19 May 1993
|
||||
# DEC Alpha, Solaris supported
|
||||
#
|
||||
# Written by sd@uk.ac.cam.mrc-lmb
|
||||
#
|
||||
|
||||
# prelim
|
||||
set prog = $0 ; set prog = $prog:t
|
||||
|
||||
# Machines supported: al sun dec sgi alpha solaris
|
||||
#set MACHINE = `echo $prog | sed 's/.*-//'`
|
||||
set MACHINE = sun
|
||||
|
||||
# For local (MRC-LMB) setup only
|
||||
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
|
||||
set LOCAL = NO
|
||||
|
||||
|
||||
echo ""
|
||||
echo -n "Staden Package installation procedure - "
|
||||
switch (${MACHINE})
|
||||
case "al":
|
||||
echo "Alliant FX/2800 Concentrix version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "sun":
|
||||
echo "SunOS version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
case "dec":
|
||||
echo "DEC Ultrix (mips) version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "sgi":
|
||||
echo "Silicon Graphics Iris version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "alpha":
|
||||
echo "DEC Alpha OSF/1 version"
|
||||
set MAKE = "gmake -sk"
|
||||
breaksw
|
||||
case "solaris":
|
||||
echo "Solaris version"
|
||||
set MAKE = "make -sk"
|
||||
breaksw
|
||||
default:
|
||||
echo "Panic. Unknown version"
|
||||
exit 1
|
||||
endsw
|
||||
echo ""
|
||||
echo "* starting initialization...please wait."
|
||||
echo ""
|
||||
|
||||
# Binary fork of source directory
|
||||
if ($LOCAL == "YES") then
|
||||
set DIR_BINARIES = ${MACHINE}-binaries
|
||||
set DIR_PROGS = ${MACHINE}-bin
|
||||
else
|
||||
set DIR_BINARIES = .
|
||||
set DIR_PROGS = bin
|
||||
set MAKE = "$MAKE -f makefile-${MACHINE}"
|
||||
endif
|
||||
|
||||
init:
|
||||
# Set useful shell variables
|
||||
set YES="YES";
|
||||
set NO="NO"
|
||||
|
||||
# set/unset some .cshrc envs.
|
||||
unset noclobber
|
||||
set noglob
|
||||
|
||||
# set interrupt trap
|
||||
onintr end_failure
|
||||
|
||||
# Make dir command
|
||||
set MKDIR = "mkdir"
|
||||
|
||||
# Copy command
|
||||
set CP = "cp -p"
|
||||
|
||||
# Install command
|
||||
#set INSTALL = "install"
|
||||
#set INSTALL = "mv"
|
||||
set INSTALL = "cp"
|
||||
|
||||
# Set up default responses
|
||||
set DEF_STADEN_ROOT = `pwd`
|
||||
|
||||
set DEF_REQ_NONX = "$YES"
|
||||
set DEF_REQ_X = "$YES"
|
||||
set DEF_REQ_TED = "$YES"
|
||||
set DEF_REQ_MISC = "$YES"
|
||||
|
||||
# directories
|
||||
set DIR_SRC = $DEF_STADEN_ROOT/src
|
||||
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
|
||||
set DIR_MISC = $DIR_SRC/Misc
|
||||
set DIR_STADEN = $DIR_SRC/staden
|
||||
set DIR_TED = $DIR_SRC/ted
|
||||
set DIR_ABI = $DIR_SRC/abi
|
||||
set DIR_ALF = $DIR_SRC/alf
|
||||
set DIR_BAP = $DIR_SRC/bap
|
||||
set DIR_OSP = $DIR_SRC/bap/osp-bits
|
||||
set DIR_CONVERT = $DIR_SRC/convert
|
||||
set DIR_COP = $DIR_SRC/cop
|
||||
set DIR_FROG = $DIR_SRC/frog
|
||||
set DIR_GETMCH = $DIR_SRC/getMCH
|
||||
set DIR_SCF = $DIR_SRC/scf
|
||||
|
||||
|
||||
main:
|
||||
|
||||
|
||||
preamble:
|
||||
echo ""
|
||||
echo ""
|
||||
echo "* Please answer the following questions."
|
||||
echo " Default answers to questions are given in square brackets."
|
||||
echo " If you require help at any stage respond with a ? to the question."
|
||||
echo ""
|
||||
|
||||
ask_staden_root:
|
||||
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
|
||||
|
||||
ask_require_nonx_progs:
|
||||
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
|
||||
set ANS_REQ_NONX = $<
|
||||
if ("$ANS_REQ_NONX" == "?") then
|
||||
echo "* If you do not have X windows on your system you will require"
|
||||
echo " these. However, you will require Tektronics terminal emulation."
|
||||
echo " If you do not require all of the non-X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
echo ""
|
||||
goto ask_require_nonx_progs
|
||||
else if ("$ANS_REQ_NONX" != "") then
|
||||
if ("$ANS_REQ_NONX" =~ [yY]*) then
|
||||
set ANS_REQ_NONX=$YES
|
||||
else if ("$ANS_REQ_NONX" =~ [nN]*) then
|
||||
set ANS_REQ_NONX=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_NONX=$DEF_REQ_NONX
|
||||
endif
|
||||
|
||||
ask_require_x_progs:
|
||||
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
|
||||
set ANS_REQ_X = $<
|
||||
if ("$ANS_REQ_X" == "?") then
|
||||
echo "* These are the programs that require X windows."
|
||||
echo " If you do not require all of the X programs, you should abort"
|
||||
echo " and manually make the ones you require."
|
||||
|
||||
echo ""
|
||||
goto ask_require_x_progs
|
||||
else if ("$ANS_REQ_X" != "") then
|
||||
if ("$ANS_REQ_X" =~ [yY]*) then
|
||||
set ANS_REQ_X=$YES
|
||||
else if ("$ANS_REQ_X" =~ [nN]*) then
|
||||
set ANS_REQ_X=$NO
|
||||
else
|
||||
goto ask_require_nonx_progs
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_X=$DEF_REQ_X
|
||||
endif
|
||||
|
||||
|
||||
ask_require_ted:
|
||||
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
|
||||
set ANS_REQ_TED = $<
|
||||
if ("$ANS_REQ_TED" == "?") then
|
||||
echo "* This is the trace editor program. It allows you to look at"
|
||||
echo " traces obtained from automated fluorescent sequencing machines."
|
||||
echo ""
|
||||
goto ask_require_ted
|
||||
else if ("$ANS_REQ_TED" != "") then
|
||||
if ("$ANS_REQ_TED" =~ [yY]*) then
|
||||
set ANS_REQ_TED=$YES
|
||||
else if ("$ANS_REQ_TED" =~ [nN]*) then
|
||||
set ANS_REQ_TED=$NO
|
||||
else
|
||||
goto ask_require_ted
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_TED=$DEF_REQ_TED
|
||||
endif
|
||||
|
||||
|
||||
|
||||
ask_require_misc:
|
||||
echo -n "Compile other programs [$DEF_REQ_MISC]? "
|
||||
set ANS_REQ_MISC = $<
|
||||
if ("$ANS_REQ_MISC" == "?") then
|
||||
echo "* Other programs include:"
|
||||
echo " alfsplit"
|
||||
echo " getABISampleName"
|
||||
echo ""
|
||||
goto ask_require_misc
|
||||
else if ("$ANS_REQ_MISC" != "") then
|
||||
if ("$ANS_REQ_MISC" =~ [yY]*) then
|
||||
set ANS_REQ_MISC=$YES
|
||||
else if ("$ANS_REQ_MISC" =~ [nN]*) then
|
||||
set ANS_REQ_MISC=$NO
|
||||
else
|
||||
goto ask_require_misc
|
||||
endif
|
||||
else
|
||||
set ANS_REQ_MISC=$DEF_REQ_MISC
|
||||
endif
|
||||
|
||||
|
||||
|
||||
time_taken_warning:
|
||||
echo ""
|
||||
echo "The installation procedure is now ready to start."
|
||||
echo ""
|
||||
echo "**** Warning:"
|
||||
echo " The installation will take considerable time to complete. If you"
|
||||
echo " are installing the whole Staden Package from scratch it could"
|
||||
echo " take as long as an hour for all exectuables to be compiled and"
|
||||
echo " installed."
|
||||
echo ""
|
||||
|
||||
ask_goahead:
|
||||
echo -n "Proceed with the installation [YES]? "
|
||||
set ANSWER=$<
|
||||
if ("$ANSWER" == "?") then
|
||||
echo "* Final confirmation to proceed with the installation. Answer"
|
||||
echo " YES to proceed; otherwise, answer NO to abort the installation."
|
||||
echo ""
|
||||
goto ask_goahead
|
||||
else if ("$ANSWER" != "") then
|
||||
if ("$ANSWER" =~ [nN]*) then
|
||||
goto chickens_exit
|
||||
else if ("$ANSWER" !~ [yY]*) then
|
||||
goto ask_goahead
|
||||
endif
|
||||
endif
|
||||
|
||||
installation_proper:
|
||||
|
||||
# make binaries directory if it doesn't exist
|
||||
|
||||
if (! -d $DIR_BIN) then
|
||||
$MKDIR $DIR_BIN
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
|
||||
echo ""
|
||||
echo "+ Compiling miscellaneous library"
|
||||
|
||||
pushd $DIR_MISC > /dev/null
|
||||
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_NONX" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing non X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE nprogs lprogs
|
||||
$INSTALL mep $DIR_BIN
|
||||
$INSTALL nip $DIR_BIN
|
||||
$INSTALL pip $DIR_BIN
|
||||
$INSTALL sap $DIR_BIN
|
||||
$INSTALL sapf $DIR_BIN
|
||||
$INSTALL sip $DIR_BIN
|
||||
$INSTALL splitp1 $DIR_BIN
|
||||
$INSTALL splitp2 $DIR_BIN
|
||||
$INSTALL splitp3 $DIR_BIN
|
||||
$INSTALL sethelp $DIR_BIN
|
||||
$INSTALL gip $DIR_BIN
|
||||
$INSTALL nipl $DIR_BIN
|
||||
$INSTALL pipl $DIR_BIN
|
||||
$INSTALL sipl $DIR_BIN
|
||||
$INSTALL dap $DIR_BIN
|
||||
$INSTALL nipf $DIR_BIN
|
||||
$INSTALL vep $DIR_BIN
|
||||
$INSTALL rep $DIR_BIN
|
||||
$INSTALL lip $DIR_BIN
|
||||
#$INSTALL convert_project $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE bap
|
||||
$INSTALL bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_TED" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing Trace editor"
|
||||
|
||||
pushd $DIR_TED > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE ted
|
||||
$INSTALL ted $DIR_BIN
|
||||
popd > /dev/null
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_X" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing X programs"
|
||||
|
||||
pushd $DIR_STADEN > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xprogs
|
||||
$INSTALL xmep $DIR_BIN
|
||||
$INSTALL xnip $DIR_BIN
|
||||
$INSTALL xpip $DIR_BIN
|
||||
$INSTALL xsap $DIR_BIN
|
||||
$INSTALL xsip $DIR_BIN
|
||||
$INSTALL xdap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_OSP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_BAP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE xbap
|
||||
$INSTALL xbap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
|
||||
endif
|
||||
|
||||
if ("$ANS_REQ_MISC" == "$YES") then
|
||||
echo ""
|
||||
echo "+ Installing miscellaneous programs"
|
||||
|
||||
pushd $DIR_ABI > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL getABISampleName $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_ALF > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE alfsplit
|
||||
$INSTALL alfsplit $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_CONVERT > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE convert
|
||||
$INSTALL convert $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_COP > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE all
|
||||
$INSTALL cop $DIR_BIN
|
||||
$INSTALL cop-bap $DIR_BIN
|
||||
popd > /dev/null
|
||||
|
||||
pushd $DIR_FROG > /dev/null
|
||||
cd $DIR_BINARIES
|
||||
$MAKE frog
|
||||
$INSTALL frog $DIR_BIN
|
||||
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
|
||||
|
BIN
bin/alfsplit
BIN
bin/convert
BIN
bin/cop-bap
BIN
bin/makeSCF
BIN
bin/sethelp
BIN
bin/splitp1
BIN
bin/splitp2
BIN
bin/splitp3
BIN
bin/trace2seq
After Width: | Height: | Size: 61 KiB |
After Width: | Height: | Size: 61 KiB |
After Width: | Height: | Size: 60 KiB |
After Width: | Height: | Size: 61 KiB |
After Width: | Height: | Size: 58 KiB |
After Width: | Height: | Size: 69 KiB |
|
@ -0,0 +1,221 @@
|
|||
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sodipodi:docname="staden-lg.svg"
|
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|
||||
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|
||||
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|
||||
id="path66"
|
||||
style="stroke-width:2.31" />
|
||||
<path
|
||||
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id="path68"
|
||||
style="stroke-width:2.31" />
|
||||
<path
|
||||
d="M27 103 c-25 -4 -27 -8 -27 -54 0 -48 1 -49 30 -49 30 0 30 1 30 55 0 30 -1 54 -2 54 -2 -1 -15 -4 -31 -6z"
|
||||
id="path98" />
|
||||
<text
|
||||
xml:space="preserve"
|
||||
transform="matrix(17.325,0,0,-17.325,-10275.938,15777.532)"
|
||||
id="text441"
|
||||
style="font-weight:bold;font-size:192px;line-height:0.6;font-family:Arial;-inkscape-font-specification:'Arial Bold';white-space:pre;shape-inside:url(#rect443);display:inline;fill:#97d5dc;stroke:#ffffff;stroke-width:9.33333;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:0;stroke-dasharray:none;paint-order:stroke markers fill"
|
||||
x="186.71935"
|
||||
y="0"><tspan
|
||||
x="700.24452"
|
||||
y="768.83587"
|
||||
id="tspan544"><tspan
|
||||
style="font-size:106.667px;font-family:Tred;-inkscape-font-specification:'Tred Bold';text-align:center;text-anchor:middle;opacity:1;fill:#000000;stroke:#000000"
|
||||
id="tspan542">STADEN
|
||||
</tspan></tspan><tspan
|
||||
x="828.26575"
|
||||
y="884.03588"
|
||||
id="tspan548"><tspan
|
||||
style="font-size:106.667px;font-family:Tred;-inkscape-font-specification:'Tred Bold';text-align:center;text-anchor:middle;opacity:1;fill:#000000;stroke:#000000"
|
||||
id="tspan546">LG</tspan></tspan></text>
|
||||
<text
|
||||
xml:space="preserve"
|
||||
transform="matrix(7.5,0,0,-7.5,0,10240)"
|
||||
id="text475"
|
||||
style="fill:#000000;stroke:#000000;font-size:5.33333333px;-inkscape-font-specification:'Tred Bold';font-family:Tred;line-height:2.2;font-weight:bold;stroke-miterlimit:0;stroke-width:9.33333333;stroke-linejoin:round;stroke-linecap:round;paint-order:stroke markers fill;white-space:pre;shape-inside:url(#rect477)" />
|
||||
</g>
|
||||
</svg>
|
After Width: | Height: | Size: 35 KiB |
|
@ -0,0 +1,8 @@
|
|||
[Desktop Entry]
|
||||
X-Desktop-File-Install-Version=0.26
|
||||
Name=ted
|
||||
Comment=Xorg BAP
|
||||
Icon=/usr/share/icons/Xted.png
|
||||
Categories=Science
|
||||
Exec=ted
|
||||
Type=Application
|
|
@ -0,0 +1,8 @@
|
|||
[Desktop Entry]
|
||||
X-Desktop-File-Install-Version=0.26
|
||||
Name=xbap
|
||||
Comment=Xorg BAP
|
||||
Icon=/usr/share/icons/Xbap.png
|
||||
Categories=Science
|
||||
Exec=xbap
|
||||
Type=Application
|
|
@ -0,0 +1,8 @@
|
|||
[Desktop Entry]
|
||||
X-Desktop-File-Install-Version=0.26
|
||||
Name=xdap
|
||||
Comment=Xorg DAP
|
||||
Icon=/usr/share/icons/dap.png
|
||||
Categories=Science
|
||||
Exec=dbap
|
||||
Type=Application
|
|
@ -0,0 +1,8 @@
|
|||
[Desktop Entry]
|
||||
X-Desktop-File-Install-Version=0.26
|
||||
Name=xmep
|
||||
Comment=Xorg MEP
|
||||
Icon=/usr/share/icons/xmep.png
|
||||
Categories=Science
|
||||
Exec=xmep
|
||||
Type=Application
|
|
@ -0,0 +1,8 @@
|
|||
[Desktop Entry]
|
||||
X-Desktop-File-Install-Version=0.26
|
||||
Name=xsap
|
||||
Comment=Xorg SAP
|
||||
Icon=/usr/share/icons/xsap.png
|
||||
Categories=Science
|
||||
Exec=xsap
|
||||
Type=Application
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/bap
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/dap
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/mep
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPNIP=/usr/share/staden-lg/help/dap_help NIPHELP=/usr/share/staden-lg/help/NIP.HLP NIPHPNT=/usr/share/staden-lg/help/NIP.PNT NIPMARG=/usr/share/staden-lg/help/NIP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/nipf
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/sap
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xbap
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xdap
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xmep
|
|
@ -0,0 +1,2 @@
|
|||
#!/bin/bash
|
||||
env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xsap
|
|
@ -0,0 +1,52 @@
|
|||
#
|
||||
# Makefile for Miscellaneous routines - Alpha version
|
||||
|
||||
#
|
||||
# Objects made by this makefile
|
||||
#
|
||||
LIBS = misc.a
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
INCLUDES = -I$(SRC)
|
||||
|
||||
#
|
||||
# Alpha Version
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
ARFLAGS = rv
|
||||
|
||||
#
|
||||
# Objects
|
||||
#
|
||||
OBJS = \
|
||||
crash.o \
|
||||
date.o \
|
||||
filenames.o \
|
||||
files.o \
|
||||
find.o \
|
||||
shell.o \
|
||||
strings.o
|
||||
|
||||
#
|
||||
# Main dependency
|
||||
#
|
||||
$(LIBS) : $(OBJS)
|
||||
/bin/rm -f $(LIBS) ;\
|
||||
$(AR) $(ARFLAGS) $(LIBS) $(OBJS) ;\
|
||||
ranlib $(LIBS)
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
all : $(LIBS)
|
||||
|
||||
clean :
|
||||
/bin/rm -f $(OBJS) $(LIBS)
|
BIN
src/abi/2rs
|
@ -0,0 +1,43 @@
|
|||
#
|
||||
# Makefile for abi - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = getABISampleName 2rs
|
||||
all: $(PROGS)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g -I$(SRC)/../ted
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
|
||||
#
|
||||
# Make the programs
|
||||
#
|
||||
getABISampleName: getABISampleName.o
|
||||
$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
|
||||
|
||||
2rs: 2rs.o
|
||||
$(LD) $(LDFLAGS) -o 2rs 2rs.o
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(PROGS) *.o *~
|
|
@ -0,0 +1,43 @@
|
|||
#
|
||||
# Makefile for alf - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = alfsplit
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g -I$(SRC)/../ted
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
|
||||
|
||||
#
|
||||
# Make the programs
|
||||
#
|
||||
alfsplit: alfsplit.o
|
||||
$(LD) $(LDFLAGS) -o alfsplit alfsplit.o $(LIBS)
|
||||
|
||||
2rs: 2rs.o
|
||||
$(LD) $(LDFLAGS) -o 2rs 2rs.o $(LIBS)
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(PROGS) *.o *~
|
||||
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
|
@ -93,8 +93,9 @@ C DBAUTO
|
|||
CALL OPENGR(DEVNOS(10))
|
||||
WRITE(KBOUT,1000)
|
||||
1000 FORMAT(
|
||||
+' BAP (Development assembly program) V12.1 May 1993',/,
|
||||
+' Copyright: MRC Laboratory of Molecular Biology')
|
||||
+' BAP (Development assembly program) V12.1.1 2023',/,
|
||||
+' Copyright: 1993 MRC Laboratory of Molecular Biology',/,
|
||||
+' Copyleft: 2023 GPL')
|
||||
IGORT = 0
|
||||
IDEV = KBOUT
|
||||
C GET SCREEN AND MARGIN SIZES
|
||||
|
|
|
@ -0,0 +1,580 @@
|
|||
# Makefile for staden X programs (Alpha version)
|
||||
# ---------------------------------------------------------
|
||||
|
||||
# This makefile generates the following staden programs which
|
||||
# run under xterm (normal, `N') and those which run directly under X.
|
||||
NPROGS= mep nip bap sap sip splitp1 splitp2 splitp3 sethelp
|
||||
LPROGS= nipl
|
||||
XPROGS= xmep xnip xbap xsap xsip
|
||||
PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# ``Interesting'' suffices that make needs to know about
|
||||
#
|
||||
.SUFFIXES: .a $(SUFFIXES)
|
||||
|
||||
|
||||
#
|
||||
# Directories
|
||||
#
|
||||
SRC = .
|
||||
STADENSRC=$(SRC)/../staden
|
||||
STADENBIN=$(STADENSRC)
|
||||
TEDSRC=$(SRC)/../ted
|
||||
TEDBIN=$(TEDSRC)
|
||||
OSPSRC=$(SRC)/osp-bits
|
||||
OSPBIN=$(OSPSRC)
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
# Use the ted sources compiled for staden executables
|
||||
INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
|
||||
|
||||
|
||||
#
|
||||
# Compilers and flags
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g -fdec -std=legacy -C
|
||||
|
||||
#FLIBS= -lfor -lUfor -lots -lFutil
|
||||
FLIBS = -lm -lutil
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(XLIBS) $(FLIBS)
|
||||
|
||||
LD = gfortran
|
||||
XLD = cc
|
||||
LDFLAGS = -g -fdec -std=legacy -L/usr/lib -lgfortran
|
||||
|
||||
#
|
||||
# Avoid compilation of objects in remote directories
|
||||
#
|
||||
$(STADENBIN)/%.o : $(STADENSRC)/%.f
|
||||
$(STADENBIN)/%.o : $(STADENSRC)/%.c
|
||||
$(TEDBIN)/%.o : $(TEDSRC)/%.f
|
||||
$(TEDBIN)/%.o : $(TEDSRC)/%.c
|
||||
|
||||
#
|
||||
# Sequence library handling routines
|
||||
#
|
||||
SEQLIB=\
|
||||
$(STADENBIN)/seqlibsubs.o
|
||||
|
||||
|
||||
|
||||
#
|
||||
# The C objects, needed by every X program
|
||||
#
|
||||
CCORE=\
|
||||
$(STADENBIN)/postscript.o\
|
||||
$(TEDBIN)/Graph.o\
|
||||
$(STADENBIN)/plotLog.o\
|
||||
$(STADENBIN)/help.o\
|
||||
$(STADENBIN)/dialogues.o\
|
||||
$(STADENBIN)/userfacecom.o\
|
||||
$(STADENBIN)/xmenu.o\
|
||||
$(STADENBIN)/locks.o\
|
||||
$(STADENBIN)/mcspec.o\
|
||||
$(STADENBIN)/helpnmenu.o\
|
||||
$(STADENBIN)/FtoC.o
|
||||
|
||||
COBJS=\
|
||||
$(STADENBIN)/main.o\
|
||||
$(CCORE)
|
||||
|
||||
COBJS2=\
|
||||
xbapmain.o\
|
||||
$(CCORE)
|
||||
|
||||
|
||||
#
|
||||
# Common objects, needed by every program
|
||||
#
|
||||
COMMONOBJSB=\
|
||||
$(STADENBIN)/fmain.o\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/nxspec.o\
|
||||
$(STADENBIN)/userface.o\
|
||||
$(STADENBIN)/userfacecom.o\
|
||||
$(STADENBIN)/nxhelpmenu.o\
|
||||
$(STADENBIN)/helpnmenu.o\
|
||||
$(STADENBIN)/FtoC.o\
|
||||
$(STADENBIN)/subs89.a
|
||||
|
||||
COMMONOBJS=\
|
||||
$(COMMONOBJSB)\
|
||||
$(STADENBIN)/postscript.o
|
||||
|
||||
SCOMMONOBJS=\
|
||||
$(COMMONOBJSB)
|
||||
|
||||
XCOMMONOBJS=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/xspec.o\
|
||||
$(STADENBIN)/subs89.a\
|
||||
$(COBJS)
|
||||
|
||||
XCOMMONOBJS2=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/xspec.o\
|
||||
$(STADENBIN)/subs89.a\
|
||||
$(COBJS2)
|
||||
|
||||
|
||||
#
|
||||
# Building the programs
|
||||
# This should be just a linking phase because all of the object
|
||||
# files and library files are generated using implicit rules.
|
||||
# We use the fortran compiler to do linking.
|
||||
#
|
||||
GIP=\
|
||||
$(STADENBIN)/gip.o
|
||||
|
||||
GIPOBJS=\
|
||||
$(GIP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
gip: $(GIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
MEP=\
|
||||
$(STADENBIN)/mep.o\
|
||||
$(STADENBIN)/mepsub.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
MEPOBJS=\
|
||||
$(MEP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XMEPOBJS=\
|
||||
$(MEP)\
|
||||
$(STADENBIN)/xmepSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
mep: $(MEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(MEPOBJS) $(LFLAGS)
|
||||
|
||||
xmep: $(XMEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
NIP=\
|
||||
$(STADENBIN)/nip.o\
|
||||
$(STADENBIN)/patternn.a\
|
||||
$(STADENBIN)/patternnc.a\
|
||||
$(STADENBIN)/anals89.a\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a $(SEQLIB)
|
||||
|
||||
NIPOBJS=\
|
||||
$(NIP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XNIPOBJS=\
|
||||
$(NIP)\
|
||||
$(STADENBIN)/xnipSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
nip: $(NIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
|
||||
|
||||
xnip: $(XNIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
NIPL=\
|
||||
$(STADENBIN)/nipl.o\
|
||||
$(STADENBIN)/patternnc.a\
|
||||
$(STADENBIN)/anals89.a\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
NIPLOBJS=\
|
||||
$(NIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
nipl: $(NIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
PIP=\
|
||||
$(STADENBIN)/pip.o\
|
||||
$(STADENBIN)/analps89.a\
|
||||
$(STADENBIN)/patternp.a\
|
||||
$(STADENBIN)/patternpc.a\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
PIPOBJS=\
|
||||
$(PIP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XPIPOBJS=\
|
||||
$(PIP)\
|
||||
$(STADENBIN)/xpipSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
pip: $(PIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPOBJS) $(LFLAGS)
|
||||
|
||||
xpip:$(XPIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
PIPL=\
|
||||
$(STADENBIN)/pipl.o\
|
||||
$(STADENBIN)/patternpc.a\
|
||||
$(STADENBIN)/analps89.a\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
PIPLOBJS=\
|
||||
$(PIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
pipl: $(PIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Trace manager objects
|
||||
#
|
||||
STDTEDFILES=\
|
||||
$(TEDBIN)/seq.o\
|
||||
$(TEDBIN)/seqIOABI.o\
|
||||
$(TEDBIN)/seqIOALF.o\
|
||||
$(TEDBIN)/seqIOSCF.o\
|
||||
$(TEDBIN)/seqIOPlain.o\
|
||||
$(TEDBIN)/opp.o\
|
||||
$(TEDBIN)/fpoint.o\
|
||||
$(TEDBIN)/mach-io.o
|
||||
|
||||
TMANOBJS=\
|
||||
$(STADENBIN)/tman_main.o\
|
||||
$(STADENBIN)/tman_display.o\
|
||||
$(STADENBIN)/tman_traceDisplay.o\
|
||||
$(STADENBIN)/tman_basesDisplay.o\
|
||||
$(STADENBIN)/tman_context.o\
|
||||
$(STADENBIN)/tman_gadgets.o\
|
||||
$(STDTEDFILES)
|
||||
|
||||
OSPOBJS=\
|
||||
$(OSPBIN)/analysis.o\
|
||||
$(OSPBIN)/our_allo.o\
|
||||
$(OSPBIN)/paramIOX.o\
|
||||
$(OSPBIN)/paramIO.o\
|
||||
$(OSPBIN)/get_scores.o\
|
||||
$(OSPBIN)/utils.o\
|
||||
mess.o\
|
||||
$(GNULIB)
|
||||
|
||||
XHACK=\
|
||||
$(STADENBIN)/SmeLine.o
|
||||
|
||||
EDITOR=\
|
||||
$(XHACK)\
|
||||
$(STADENBIN)/xsapConEdit.o\
|
||||
contigEditor.o\
|
||||
edUtils.o\
|
||||
$(STADENBIN)/undo.o\
|
||||
$(STADENBIN)/Sheet.o\
|
||||
$(STADENBIN)/select.o\
|
||||
$(STADENBIN)/extend.o\
|
||||
$(STADENBIN)/searchUtils.o\
|
||||
edMenu.o\
|
||||
oligo.o\
|
||||
oligocom.o\
|
||||
subclone.o\
|
||||
myparams.o\
|
||||
$(STADENBIN)/trans.o\
|
||||
$(MISCBIN)/misc.a
|
||||
|
||||
TAGEDITOR=\
|
||||
$(STADENBIN)/tagEditor.o\
|
||||
$(STADENBIN)/tagdbparse.o\
|
||||
tagU2.o\
|
||||
$(STADENBIN)/tagU1.o
|
||||
|
||||
BAP=\
|
||||
bap.o\
|
||||
dbsysnew.o\
|
||||
dbsyscommon.o\
|
||||
actf.o\
|
||||
dstrand.o\
|
||||
oligo_sel.o\
|
||||
llin.o\
|
||||
guk.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
BAPOBJS=\
|
||||
$(BAP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o\
|
||||
$(STADENBIN)/conEdit.o\
|
||||
tagU2.o\
|
||||
$(OSPBIN)/analysis.o\
|
||||
$(OSPBIN)/our_allo.o\
|
||||
$(OSPBIN)/get_scores.o\
|
||||
$(OSPBIN)/utils.o\
|
||||
mess.o\
|
||||
baponly.o\
|
||||
oligocom.o
|
||||
|
||||
XBAPOBJS=\
|
||||
$(BAP)\
|
||||
$(XCOMMONOBJS2)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o\
|
||||
$(EDITOR)\
|
||||
$(TMANOBJS)\
|
||||
$(TAGEDITOR)\
|
||||
$(OSPOBJS)
|
||||
|
||||
bap: $(BAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
|
||||
|
||||
xbap: $(XBAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
|
||||
|
||||
SAP=\
|
||||
sap.o\
|
||||
dbsyscommon.o\
|
||||
dbsysold.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
SAPOBJS=\
|
||||
$(SAP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XSAPOBJS=\
|
||||
$(SAP)\
|
||||
$(STADENBIN)/xsapSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
sap: $(SAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
|
||||
|
||||
xsap: $(XSAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SAPF=\
|
||||
$(STADENBIN)/sapf.o\
|
||||
$(STADENBIN)/dbsyscommon.o\
|
||||
$(STADENBIN)/dbsysold.o\
|
||||
$(STADENBIN)/asubs89.a\
|
||||
$(STADENBIN)/plot92.a
|
||||
|
||||
SAPFOBJS=\
|
||||
$(SAPF)\
|
||||
$(STADENBIN)/sapmen.o\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
sapf: $(SAPFOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SIP=\
|
||||
$(STADENBIN)/sip.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
$(STADENBIN)/plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPOBJS=\
|
||||
$(SIP)\
|
||||
$(COMMONOBJS)\
|
||||
$(STADENBIN)/pl4010.o
|
||||
|
||||
XSIPOBJS=\
|
||||
$(SIP)\
|
||||
$(STADENBIN)/xsipSpec.o\
|
||||
$(XCOMMONOBJS)\
|
||||
$(STADENBIN)/plX.o\
|
||||
$(STADENBIN)/textOutput.o
|
||||
|
||||
sip: $(SIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
|
||||
|
||||
xsip: $(XSIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SIPL=\
|
||||
$(STADENBIN)/sipl.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPLOBJS=\
|
||||
$(SIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
sipl: $(SIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SETHELP=\
|
||||
$(STADENBIN)/sethelp.o
|
||||
|
||||
SETHELPOBJS=\
|
||||
$(SETHELP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
sethelp: $(SETHELPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP1=\
|
||||
$(STADENBIN)/splitp1.o
|
||||
SPLITP1OBJS=\
|
||||
$(SPLITP1)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp1: $(SPLITP1OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP2=\
|
||||
$(STADENBIN)/splitp2.o
|
||||
SPLITP2OBJS=\
|
||||
$(SPLITP2)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp2: $(SPLITP2OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP3=\
|
||||
$(STADENBIN)/splitp3.o
|
||||
SPLITP3OBJS=\
|
||||
$(SPLITP3)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp3: $(SPLITP3OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.f
|
||||
$(F77) $(FFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o: %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# The UNIX library (archive) mechanism is fairly weak so the following
|
||||
# procedure is used to generate libraries.
|
||||
# * split the source file up into files which each contain
|
||||
# a single function or subroutine
|
||||
# * compile each of those files
|
||||
# * insert the object files individually into the library
|
||||
# Each library is built by using a temporary directory.
|
||||
# The fortran compilations must be done sequentially in order to
|
||||
# avoid filling up the (small on this machine) /tmp directory
|
||||
# with compiler debugging information.
|
||||
#
|
||||
#%.a: $(SRC)/%.f
|
||||
# BINDIR=`pwd`; \
|
||||
# cd $(SRC); \
|
||||
# SRCDIR=`pwd`; \
|
||||
# TMPDIR=/tmp/staden$$$$; \
|
||||
# if test ! -d $$TMPDIR; \
|
||||
# then mkdir $$TMPDIR; \
|
||||
# fi; \
|
||||
# cd $$TMPDIR; \
|
||||
# rm -f *.f *.o; \
|
||||
# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
# $(F77) $(FFLAGS) -c *.f; \
|
||||
# rm *.f; \
|
||||
# rm -f $$BINDIR/$@; \
|
||||
# ar rcv $$BINDIR/$@ *.o; \
|
||||
# ranlib $$BINDIR/$@; \
|
||||
# rm *.o; \
|
||||
# cd $$BINDIR; \
|
||||
# rm -r $$TMPDIR
|
||||
|
||||
|
||||
#%.a: $(SRC)/%.f
|
||||
# $(F77) $(FFLAGS) -c *.f;
|
||||
# ar rcv $$BINDIR/$@ *.o;
|
||||
|
||||
|
||||
|
||||
all: $(NPROGS) $(XPROGS) $(LPROGS)
|
||||
|
||||
nprogs: $(NPROGS)
|
||||
|
||||
xprogs: $(XPROGS)
|
||||
|
||||
lprogs: $(LPROGS)
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) *.o *.a *~
|
|
@ -1,8 +1,8 @@
|
|||
/*
|
||||
/*
|
||||
Program Name: mess
|
||||
File name: mess.c
|
||||
Purpose: put user information to the screen for the text version
|
||||
of osp--maybe error messages or any kind of user information
|
||||
of osp--maybe error messages or any kind of user information
|
||||
or question.
|
||||
|
||||
Last Update: Tuesday 13 August 1991
|
||||
|
@ -15,47 +15,50 @@
|
|||
*/
|
||||
|
||||
/* --- includes --- */
|
||||
#include "defn.h" /* IMPORT: stdio.h */
|
||||
#include "textOutput.h" /* IMPORT: UpdateTextOutput */
|
||||
#include <stdio.h>
|
||||
#include <stdarg.h>
|
||||
/* int vfprintf (FILE *stream, const char *format, va_list arglist); */
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
#include "defn.h" /* IMPORT: stdio.h */
|
||||
#include "textOutput.h" /* IMPORT: UpdateTextOutput */
|
||||
/* int vfprintf (FILE *stream, const char *format, va_list arglist);
|
||||
*/
|
||||
|
||||
/* ---- Exports ---- */
|
||||
void messagef(char *format, ...)
|
||||
{
|
||||
va_list args;
|
||||
va_start (args,format);
|
||||
vfprintf (stdout, format, args);
|
||||
va_end(args);
|
||||
UpdateTextOutput();
|
||||
va_list args;
|
||||
va_start(args, format);
|
||||
vfprintf(stdout, format, args);
|
||||
va_end(args);
|
||||
UpdateTextOutput();
|
||||
}
|
||||
|
||||
void message(char *message)
|
||||
{
|
||||
/* prints the message to the screen*/
|
||||
fprintf(stdout,"%s",message);
|
||||
UpdateTextOutput();
|
||||
return;
|
||||
/* prints the message to the screen*/
|
||||
fprintf(stdout, "%s", message);
|
||||
UpdateTextOutput();
|
||||
return;
|
||||
}
|
||||
|
||||
void popupMessage(char *message)
|
||||
{
|
||||
fprintf(stdout,"%s",message);
|
||||
UpdateTextOutput();
|
||||
return;
|
||||
fprintf(stdout, "%s", message);
|
||||
UpdateTextOutput();
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
void popUpErrorMessage()
|
||||
{
|
||||
fprintf(stdout,"ERROR: Memory allocation problem.\nPlease exit and restart this program\n");
|
||||
/* since this is the text version I want the program to exit if this
|
||||
memory allocation error occurs*/
|
||||
UpdateTextOutput();
|
||||
sleep(10);
|
||||
|
||||
exit();
|
||||
fprintf(stdout,
|
||||
"ERROR: Memory allocation problem.\nPlease exit and restart "
|
||||
"this program\n");
|
||||
/* since this is the text version I want the program to exit if this
|
||||
memory allocation error occurs*/
|
||||
UpdateTextOutput();
|
||||
sleep(10);
|
||||
|
||||
exit(0);
|
||||
}
|
||||
|
||||
|
|
|
@ -0,0 +1,50 @@
|
|||
#
|
||||
# Makefile for osp (oligo selection program) - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = subosp
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# X VERSION compilation flag
|
||||
#
|
||||
VERSION = SUBVERSION
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g -D$(VERSION)
|
||||
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
XOSPOBJS= our_allo.o analysis.o get_scores.o paramIO.o paramIOX.o utils.o
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
subosp: $(XOSPOBJS)
|
||||
|
||||
|
||||
#
|
||||
# Miscellaneous
|
||||
#
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) $(OSPOBJS) *~
|
||||
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
#
|
||||
# Makefile for convert (Alpha version)
|
||||
#
|
||||
|
||||
SRC = .
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
|
||||
CC = cc
|
||||
CFLAGS = -g -I$(MISCSRC)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LIBS = $(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = convert
|
||||
|
||||
all : $(PROGS)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
|
||||
OBJS = \
|
||||
list.o \
|
||||
main.o \
|
||||
dapIO.o \
|
||||
dapDB.o \
|
||||
bapIO.o \
|
||||
bapDB.o \
|
||||
process.o \
|
||||
flat_sd.o
|
||||
|
||||
convert: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o convert $(OBJS) $(LIBS) $(LDFLAGS)
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
%.o:$(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
clean :
|
||||
/bin/rm -f $(PROGS) $(OBJS) *~
|
|
@ -0,0 +1,114 @@
|
|||
#
|
||||
# Makefile for COP (Check Out Project) - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = cop cop-bap
|
||||
all: $(PROGS)
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
MISCSRC = $(SRC)/../Misc
|
||||
MISCBIN = $(MISCSRC)
|
||||
CONVERTSRC = $(SRC)/../convert
|
||||
INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LIBFLAGS =
|
||||
|
||||
#
|
||||
# Main and miscellaneous routines
|
||||
#
|
||||
COPOBJ = \
|
||||
cop.o
|
||||
|
||||
COPBAPOBJ = \
|
||||
cop-bap.o
|
||||
|
||||
LIBS = \
|
||||
$(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
# For reading in xdap database
|
||||
#
|
||||
XDAPIO = \
|
||||
dapIO.o
|
||||
|
||||
XBAPIO = \
|
||||
bapIO.o
|
||||
|
||||
#
|
||||
# For reading in trace files
|
||||
#
|
||||
TRACES = \
|
||||
getSeq.o \
|
||||
seqIOABI.o \
|
||||
seqIOALF.o \
|
||||
seqIOSCF.o \
|
||||
seqIOPlain.o \
|
||||
opp.o \
|
||||
seq.o \
|
||||
fpoint.o\
|
||||
mach-io.o
|
||||
|
||||
#
|
||||
# For aligning sequences
|
||||
#
|
||||
ALIGN = \
|
||||
llin.o
|
||||
|
||||
#
|
||||
# The whole lot
|
||||
#
|
||||
OBJ = \
|
||||
$(COPOBJ) \
|
||||
$(XDAPIO) \
|
||||
$(TRACES) \
|
||||
$(ALIGN)
|
||||
|
||||
OBJBAP = \
|
||||
$(COPBAPOBJ) \
|
||||
$(XBAPIO) \
|
||||
$(TRACES) \
|
||||
$(ALIGN)
|
||||
|
||||
|
||||
#
|
||||
# Cop
|
||||
#
|
||||
cop : $(OBJ)
|
||||
$(LD) $(LDFLAGS) -o cop $(OBJ) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
cop-bap : $(OBJBAP)
|
||||
$(LD) $(LDFLAGS) -o cop-bap $(OBJBAP) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(OBJ) $(PROGS) *~
|
||||
|
||||
cop-bap.o: $(SRC)/cop.c
|
||||
$(CC) -DBAP_VERSION $(CFLAGS) -o cop-bap.o -c $(SRC)/cop.c
|
||||
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
%.o: $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
|
@ -0,0 +1,93 @@
|
|||
#
|
||||
# Makefile for expGetSeq - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
# select a left (using the -enzyme option or the .enzyme in the
|
||||
# Xted file) and right cutoff on your sequence (using 2 out of
|
||||
# 5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
# Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
# Turning on the QUAL_CODE switch enables LaDeana's trace quality
|
||||
# clipping code.
|
||||
#
|
||||
# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
|
||||
# enables the overall trace quality check.
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS -DQUAL_CODE -DQUAL_CHECK
|
||||
SWITCHES = -DAUTO_CLIP -DQUAL_CODE
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = expGetSeq
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../newted
|
||||
INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
OBJS=\
|
||||
getMCH.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
match.o\
|
||||
mach-io.o\
|
||||
seqRead.o\
|
||||
traceType.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
expGetSeq: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
CC = cc
|
||||
CFLAGS = -g
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
LIBFLAGS =
|
||||
|
||||
SRC = .
|
||||
PROGS = frog toad
|
||||
all: $(PROGS)
|
||||
|
||||
FROGOBJ =\
|
||||
frog.o\
|
||||
mach-io.o
|
||||
|
||||
frog : $(FROGOBJ)
|
||||
$(LD) $(LDFLAGS) -o frog $(FROGOBJ) $(LIBFLAGS)
|
||||
|
||||
|
||||
TOADOBJ =\
|
||||
toad.o\
|
||||
scfIO.o\
|
||||
mach-io.o
|
||||
|
||||
toad : $(TOADOBJ)
|
||||
$(LD) $(LDFLAGS) -o toad $(TOADOBJ) $(LIBFLAGS)
|
||||
|
||||
|
||||
#
|
||||
# Specials
|
||||
#
|
||||
%.o:$(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(PROGS) $(FROGOBJ)
|
|
@ -0,0 +1,86 @@
|
|||
#
|
||||
# Makefile for getMCH - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
#Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
#select a left (using the -enzyme option or the .enzyme in the
|
||||
#Xted file) and right cutoff on your sequence (using 2 out of
|
||||
#5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
#Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = getMCH trace2seq
|
||||
all: $(PROGS)
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
INCLUDES = -I$(SRC) -I$(TEDSRC)
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LIBFLAGS =
|
||||
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
OBJS=\
|
||||
getMCH.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
match.o\
|
||||
mach-io.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
trace2seq getMCH: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o : $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
|
@ -13,7 +13,7 @@ static FILE *out;
|
|||
|
||||
static int line_comp(char *ex, char *in, int l)
|
||||
/*
|
||||
** Compare exclude line with inline
|
||||
** Compare exclude line with cinline
|
||||
*/
|
||||
{
|
||||
return strncmp(ex,in+11,l);
|
||||
|
@ -28,13 +28,13 @@ static void process()
|
|||
*/
|
||||
{
|
||||
char exline[MAXLINE];
|
||||
char inline[MAXLINE];
|
||||
char cinline[MAXLINE];
|
||||
char *exok, *inok;
|
||||
int compare;
|
||||
|
||||
|
||||
exok = fgets(exline,MAXLINE,ex);
|
||||
inok = fgets(inline,MAXLINE,in);
|
||||
inok = fgets(cinline,MAXLINE,in);
|
||||
|
||||
while (exok && inok) {
|
||||
|
||||
|
@ -43,15 +43,15 @@ static void process()
|
|||
if (compare < 0)
|
||||
exok = fgets(exline,MAXLINE,ex);
|
||||
else if (compare > 0) {
|
||||
fprintf(out,"%s",inline);
|
||||
inok = fgets(inline,MAXLINE,in);
|
||||
fprintf(out,"%s",cinline);
|
||||
inok = fgets(cinline,MAXLINE,in);
|
||||
} else
|
||||
inok = fgets(inline,MAXLINE,in);
|
||||
inok = fgets(cinline,MAXLINE,in);
|
||||
|
||||
}
|
||||
|
||||
while (inok = fgets(inline,MAXLINE,in))
|
||||
fprintf(out,"%s",inline);
|
||||
while (inok = fgets(cinline,MAXLINE,in))
|
||||
fprintf(out,"%s",cinline);
|
||||
|
||||
}
|
||||
|
||||
|
|
|
@ -0,0 +1,172 @@
|
|||
#
|
||||
# indexseqlibs - Alpha version
|
||||
#
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
#
|
||||
# Programs need making
|
||||
#
|
||||
PROGS = \
|
||||
addnl \
|
||||
genbentryname1 \
|
||||
entryname2 \
|
||||
access4 \
|
||||
access2 \
|
||||
genbaccess1 \
|
||||
title2 \
|
||||
genbtitle1 \
|
||||
emblentryname1 \
|
||||
emblaccess1 \
|
||||
embltitle1 \
|
||||
pirentryname1 \
|
||||
piraccess1 \
|
||||
piraccess2 \
|
||||
pirtitle1 \
|
||||
pirtitle2 \
|
||||
excludewords \
|
||||
emblfreetext \
|
||||
genbfreetext \
|
||||
pirfreetext \
|
||||
freetext2 \
|
||||
freetext4 \
|
||||
emblauthor \
|
||||
genbauthor \
|
||||
pirauthor \
|
||||
hitNtrg \
|
||||
division
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
|
||||
#
|
||||
# Shared objects
|
||||
#
|
||||
OBJS = \
|
||||
cdromheader.o \
|
||||
mach-io.o
|
||||
|
||||
#
|
||||
# Dependencies for programs
|
||||
#
|
||||
addnl : addnl.o
|
||||
$(LD) $(LDFLAGS) -o $@ addnl.o
|
||||
|
||||
genbentryname1 : genbentryname1.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbentryname1.o
|
||||
|
||||
entryname2 : entryname2.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ entryname2.o $(OBJS)
|
||||
|
||||
access4 : access4.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ access4.o $(OBJS)
|
||||
|
||||
access2 : access2.o
|
||||
$(LD) $(LDFLAGS) -o $@ access2.o
|
||||
|
||||
genbaccess1 : genbaccess1.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbaccess1.o
|
||||
|
||||
title2 : title2.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ title2.o $(OBJS)
|
||||
|
||||
genbtitle1 : genbtitle1.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbtitle1.o
|
||||
|
||||
emblentryname1 : emblentryname1.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblentryname1.o
|
||||
|
||||
emblaccess1 : emblaccess1.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblaccess1.o
|
||||
|
||||
embltitle1 : embltitle1.o
|
||||
$(LD) $(LDFLAGS) -o $@ embltitle1.o
|
||||
|
||||
pirentryname1 : pirentryname1.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirentryname1.o
|
||||
|
||||
piraccess1 : piraccess1.o
|
||||
$(LD) $(LDFLAGS) -o $@ piraccess1.o
|
||||
|
||||
piraccess2 : piraccess2.o
|
||||
$(LD) $(LDFLAGS) -o $@ piraccess2.o
|
||||
|
||||
pirtitle1 : pirtitle1.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirtitle1.o
|
||||
|
||||
pirtitle2 : pirtitle2.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirtitle2.o
|
||||
|
||||
excludewords : excludewords.o
|
||||
$(LD) $(LDFLAGS) -o $@ excludewords.o
|
||||
|
||||
emblfreetext.o: $(SRC)/freetext.c
|
||||
$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
|
||||
emblfreetext : emblfreetext.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblfreetext.o
|
||||
|
||||
genbfreetext.o: $(SRC)/freetext.c
|
||||
$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
|
||||
genbfreetext : genbfreetext.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbfreetext.o
|
||||
|
||||
pirfreetext.o: $(SRC)/freetext.c
|
||||
$(CC) $(CFLAGS) -DPIR -c -o $@ $<
|
||||
pirfreetext : pirfreetext.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirfreetext.o
|
||||
|
||||
freetext2 : freetext2.o
|
||||
$(LD) $(LDFLAGS) -o $@ freetext2.o
|
||||
|
||||
freetext4 : freetext4.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ freetext4.o $(OBJS)
|
||||
|
||||
emblauthor.o : $(SRC)/author.c
|
||||
$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
|
||||
emblauthor : emblauthor.o
|
||||
$(LD) $(LDFLAGS) -o $@ emblauthor.o
|
||||
|
||||
genbauthor.o : $(SRC)/author.c
|
||||
$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
|
||||
genbauthor : genbauthor.o
|
||||
$(LD) $(LDFLAGS) -o $@ genbauthor.o
|
||||
|
||||
pirauthor.o : $(SRC)/author.c
|
||||
$(CC) $(CFLAGS) -DPIR -c -o $@ $<
|
||||
pirauthor : pirauthor.o
|
||||
$(LD) $(LDFLAGS) -o $@ pirauthor.o
|
||||
|
||||
hitNtrg : hitNtrg.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ hitNtrg.o $(OBJS)
|
||||
|
||||
division : division.o $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ division.o $(OBJS)
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
|
||||
|
||||
all : $(PROGS)
|
||||
|
||||
clean :
|
||||
/bin/rm -f $(PROGS) *.o *~
|
||||
|
||||
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -0,0 +1,117 @@
|
|||
#
|
||||
# Makefile for ted (trace editor) - Alpha fork
|
||||
#
|
||||
|
||||
#
|
||||
# Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
# select a left (using the -enzyme option or the .enzyme in the
|
||||
# Xted file) and right cutoff on your sequence (using 2 out of
|
||||
# 5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
# Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
# Turning on the QUAL_CODE switch enables LaDeana's trace quality
|
||||
# clipping code.
|
||||
#
|
||||
# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
|
||||
# enables the overall trace quality check.
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS -DQUAL_CODE -DQUAL_CHECK
|
||||
SWITCHES = -DAUTO_CLIP -DQUAL_CODE -DQUAL_CHECK
|
||||
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = ted autoted
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= cc
|
||||
INCLUDES = -I$(SRC)
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
TEDOBJS=\
|
||||
ted.o\
|
||||
dialogues.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
help.o\
|
||||
display.o\
|
||||
traceDisplay.o\
|
||||
basesDisplay.o\
|
||||
Graph.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
info.o\
|
||||
fpoint.o\
|
||||
mach-io.o\
|
||||
seqRead.o\
|
||||
traceType.o\
|
||||
match.o
|
||||
|
||||
AUTOTEDOBJS=\
|
||||
autoted.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
traceType.o\
|
||||
fpoint.o\
|
||||
mach-io.o\
|
||||
match.o\
|
||||
seqRead.o
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
ted: $(TEDOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
|
||||
autoted: $(AUTOTEDOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(AUTOTEDOBJS) $(LIBS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
#
|
||||
# getMCH - Alpha version
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = makeSCF
|
||||
|
||||
#
|
||||
# SWITCHES - see ted makefile
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
TEDSRC = $(SRC)/../ted
|
||||
|
||||
#
|
||||
# alpha
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(SWITCHES) -I$(TEDSRC)
|
||||
LD= cc
|
||||
LDFLAGS= -g
|
||||
LIBFLAGS =
|
||||
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
%.o : $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
OBJS=\
|
||||
makeSCF.o\
|
||||
writeSCF.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
match.o\
|
||||
mach-io.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
makeSCF: $(OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(OBJS) $(PROGS) *~
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: Sheet.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: Sheet.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: SheetP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -0,0 +1,19 @@
|
|||
#!/bin/bash
|
||||
#
|
||||
for fortran in $(ls *.f)
|
||||
do
|
||||
mkdir -p ${fortran%??}
|
||||
cp $fortran ${fortran%??}
|
||||
|
||||
cd ${fortran%??}
|
||||
fsplit ${fortran}
|
||||
rm ${fortran}
|
||||
|
||||
gfortran -g -fdec -std=legacy -C -c *.f
|
||||
ar rcv ${fortran%??}.a *.o
|
||||
ranlib ${fortran%??}.a
|
||||
|
||||
cd ..
|
||||
cp ${fortran%??}/*.a .
|
||||
rm -rf ${fortran%??}
|
||||
done
|
|
@ -0,0 +1,603 @@
|
|||
# Makefile for staden X programs (Alpha OSF/1.2 version)
|
||||
# ------------------------------------------------------
|
||||
|
||||
# This makefile generates the following staden programs which
|
||||
# run under xterm (normal, `N') and those which run directly under X.
|
||||
NPROGS= mep nip pip dap sap sip splitp1 splitp2 splitp3 gip sethelp convert_project rep lip sapf nipf vep
|
||||
LPROGS= nipl pipl sipl
|
||||
XPROGS= xmep xnip xpip xdap xsap xsip
|
||||
PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
|
||||
|
||||
#
|
||||
# ``Interesting'' suffices that make needs to know about
|
||||
#
|
||||
.SUFFIXES: .a $(SUFFIXES)
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC=.
|
||||
TEDSRC=$(SRC)/../ted
|
||||
MISCSRC=$(SRC)/../Misc
|
||||
MISCBIN=$(MISCSRC)
|
||||
INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
|
||||
|
||||
#
|
||||
# Compilers and flags
|
||||
#
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g -fdec -std=legacy -L/usr/lib -lgfortran -C
|
||||
|
||||
FLIBS = -lutil -lm
|
||||
#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(FLIBS) $(XLIBS)
|
||||
|
||||
LD = gfortran
|
||||
CLD = gfortran
|
||||
#CLD = cc
|
||||
LDFLAGS = -g # Comment out for faster linking when debugging
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Sequence library handling routines
|
||||
#
|
||||
SEQLIB=\
|
||||
seqlibsubs.o
|
||||
|
||||
|
||||
#
|
||||
# The C objects, needed by every X program
|
||||
#
|
||||
CCORE=\
|
||||
postscript.o\
|
||||
Graph.o\
|
||||
plotLog.o\
|
||||
help.o\
|
||||
dialogues.o\
|
||||
userfacecom.o\
|
||||
helpnmenu.o\
|
||||
xmenu.o\
|
||||
FtoC.o\
|
||||
mcspec.o\
|
||||
locks.o
|
||||
|
||||
COBJS=\
|
||||
main.o\
|
||||
$(CCORE)
|
||||
|
||||
XDAPCOBJS=\
|
||||
xdapmain.o\
|
||||
$(CCORE)
|
||||
|
||||
|
||||
#
|
||||
# Common objects, needed by every program
|
||||
#
|
||||
COMMONOBJSB=\
|
||||
fmain.o\
|
||||
seeme-aix.o\
|
||||
nxspec.o\
|
||||
userface.o\
|
||||
userfacecom.o\
|
||||
nxhelpmenu.o\
|
||||
helpnmenu.o\
|
||||
FtoC.o\
|
||||
subs89.a
|
||||
|
||||
COMMONOBJS=\
|
||||
$(COMMONOBJSB)\
|
||||
postscript.o
|
||||
|
||||
SCOMMONOBJS=\
|
||||
$(COMMONOBJSB)
|
||||
|
||||
XCOMMONOBJS=\
|
||||
seeme-aix.o\
|
||||
xspec.o\
|
||||
subs89.a\
|
||||
$(COBJS)
|
||||
|
||||
XDAPCOMMONOBJS=\
|
||||
seeme-aix.o\
|
||||
xspec.o\
|
||||
subs89.a\
|
||||
$(XDAPCOBJS)
|
||||
|
||||
|
||||
#
|
||||
# Building the programs
|
||||
# This should be just a linking phase because all of the object
|
||||
# files and library files are generated using implicit rules.
|
||||
# We use the fortran compiler to do linking.
|
||||
#
|
||||
GIP=\
|
||||
gip.o
|
||||
|
||||
GIPOBJS=\
|
||||
$(GIP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
gip: $(GIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
LIP=\
|
||||
lip.o
|
||||
|
||||
LIPOBJS=\
|
||||
$(LIP)\
|
||||
$(SEQLIB)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
lip: $(LIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(LIPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
MEP=\
|
||||
mep.o\
|
||||
mepsub.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
MEPOBJS=\
|
||||
$(MEP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XMEPOBJS=\
|
||||
$(MEP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
mep: $(MEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(MEPOBJS) $(LFLAGS)
|
||||
|
||||
xmep: $(XMEPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
NIP=\
|
||||
nip.o\
|
||||
patternn.a\
|
||||
patternnc.a\
|
||||
anals89.a\
|
||||
asubs89.a\
|
||||
plot92.a \
|
||||
$(SEQLIB)
|
||||
|
||||
NIPOBJS=\
|
||||
$(NIP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XNIPOBJS=\
|
||||
$(NIP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
nip: $(NIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
|
||||
|
||||
xnip: $(XNIPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
NIPL=\
|
||||
nipl.o\
|
||||
patternnc.a\
|
||||
anals89.a\
|
||||
asubs89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
NIPLOBJS=\
|
||||
$(NIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
nipl: $(NIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
NIPF=\
|
||||
nipf.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
NIPFOBJS=\
|
||||
$(NIPF)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
|
||||
nipf: $(NIPFOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(NIPFOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
PIP=\
|
||||
pip.o\
|
||||
analps89.a\
|
||||
patternp.a\
|
||||
patternpc.a\
|
||||
asubs89.a\
|
||||
plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
PIPOBJS=\
|
||||
$(PIP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XPIPOBJS=\
|
||||
$(PIP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
pip: $(PIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPOBJS) $(LFLAGS)
|
||||
|
||||
xpip:$(XPIPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
PIPL=\
|
||||
pipl.o\
|
||||
patternpc.a\
|
||||
analps89.a\
|
||||
asubs89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
PIPLOBJS=\
|
||||
$(PIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
pipl: $(PIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Trace manager objects
|
||||
#
|
||||
STDTEDFILES=\
|
||||
seq.o\
|
||||
seqIOABI.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqIOPlain.o\
|
||||
opp.o\
|
||||
fpoint.o\
|
||||
mach-io.o
|
||||
|
||||
TMANOBJS=\
|
||||
tman_main.o\
|
||||
tman_display.o\
|
||||
tman_traceDisplay.o\
|
||||
tman_basesDisplay.o\
|
||||
tman_context.o\
|
||||
tman_gadgets.o\
|
||||
$(STDTEDFILES)
|
||||
|
||||
# Some versions of X11R4 may have a bug in SmeLine.c
|
||||
XHACK=\
|
||||
SmeLine.o
|
||||
|
||||
EDITOR=\
|
||||
$(XHACK)\
|
||||
xsapConEdit.o\
|
||||
contigEditor.o\
|
||||
edUtils.o\
|
||||
undo.o\
|
||||
Sheet.o\
|
||||
select.o\
|
||||
extend.o\
|
||||
searchUtils.o\
|
||||
edMenu.o\
|
||||
trans.o\
|
||||
$(MISCBIN)/misc.a
|
||||
|
||||
TAGEDITOR=\
|
||||
tagEditor.o\
|
||||
tagdbparse.o\
|
||||
tagU2.o\
|
||||
tagU1.o
|
||||
|
||||
DAP=\
|
||||
dap.o\
|
||||
dbsysnew.o\
|
||||
dbsyscommon.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
DAPOBJS=\
|
||||
$(DAP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o\
|
||||
conEdit.o\
|
||||
tagU2.o
|
||||
|
||||
XDAPOBJS=\
|
||||
$(DAP)\
|
||||
$(XDAPCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o\
|
||||
$(EDITOR)\
|
||||
$(TMANOBJS)\
|
||||
$(TAGEDITOR)
|
||||
|
||||
dap: $(DAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(DAPOBJS) $(LFLAGS)
|
||||
|
||||
xdap: $(XDAPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XDAPOBJS) $(XLFLAGS)
|
||||
|
||||
convert_project: cvt.o
|
||||
$(CC) $(CFLAGS) -o $@ cvt.o
|
||||
|
||||
SAP=\
|
||||
sap.o\
|
||||
dbsyscommon.o\
|
||||
dbsysold.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
SAPOBJS=\
|
||||
$(SAP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XSAPOBJS=\
|
||||
$(SAP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
sap: $(SAPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
|
||||
|
||||
xsap: $(XSAPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SAPF=\
|
||||
sapf.o\
|
||||
dbsyscommon.o\
|
||||
dbsysold.o\
|
||||
asubs89.a\
|
||||
plot92.a
|
||||
|
||||
SAPFOBJS=\
|
||||
$(SAPF)\
|
||||
sapmen.o\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
sapf: $(SAPFOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SIP=\
|
||||
sip.o\
|
||||
dias89.a\
|
||||
plot92.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPOBJS=\
|
||||
$(SIP)\
|
||||
$(COMMONOBJS)\
|
||||
pl4010.o
|
||||
|
||||
XSIPOBJS=\
|
||||
$(SIP)\
|
||||
$(XCOMMONOBJS)\
|
||||
plX.o\
|
||||
textOutput.o
|
||||
|
||||
sip: $(SIPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
|
||||
|
||||
xsip: $(XSIPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SIPL=\
|
||||
sipl.o\
|
||||
dias89.a\
|
||||
$(SEQLIB)
|
||||
|
||||
SIPLOBJS=\
|
||||
$(SIPL)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
sipl: $(SIPLOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SETHELP=\
|
||||
sethelp.o
|
||||
|
||||
SETHELPOBJS=\
|
||||
$(SETHELP)
|
||||
|
||||
sethelp: $(SETHELPOBJS)
|
||||
$(CLD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP1=\
|
||||
splitp1.o
|
||||
SPLITP1OBJS=\
|
||||
$(SPLITP1)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp1: $(SPLITP1OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP2=\
|
||||
splitp2.o
|
||||
SPLITP2OBJS=\
|
||||
$(SPLITP2)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp2: $(SPLITP2OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
SPLITP3=\
|
||||
splitp3.o
|
||||
SPLITP3OBJS=\
|
||||
$(SPLITP3)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
splitp3: $(SPLITP3OBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
REP=\
|
||||
rep.o\
|
||||
dias89.a\
|
||||
subs89.a
|
||||
|
||||
REPOBJS=\
|
||||
$(REP)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
rep: $(REPOBJS)
|
||||
$(F77) $(LDFLAGS) -o $@ $(REPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
VEP=\
|
||||
vep.o\
|
||||
dias89.a\
|
||||
subs89.a
|
||||
|
||||
|
||||
VEPOBJS=\
|
||||
$(VEP)\
|
||||
$(SCOMMONOBJS)
|
||||
|
||||
|
||||
vep: $(VEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(VEPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
#
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o: $(TEDSRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.f
|
||||
$(F77) $(FFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# The UNIX library (archive) mechanism is fairly weak so the following
|
||||
# procedure is used to generate libraries.
|
||||
# * split the source file up into files which each contain
|
||||
# a single function or subroutine
|
||||
# * compile each of those files
|
||||
# * insert the object files individually into the library
|
||||
# Each library is built by using a temporary directory.
|
||||
# The fortran compilations must be done sequentially in order to
|
||||
# avoid filling up the (small on this machine) /tmp directory
|
||||
# with compiler debugging information.
|
||||
#
|
||||
%.a: $(SRC)/%.f
|
||||
sh gen_a.sh
|
||||
|
||||
# BINDIR=`pwd`; \
|
||||
# cd $(SRC); \
|
||||
# SRCDIR=`pwd`; \
|
||||
#
|
||||
# TMPDIR=/tmp/staden$$$$; \
|
||||
# if test ! -d $$TMPDIR; \
|
||||
# then mkdir $$TMPDIR; \
|
||||
# fi; \
|
||||
# cd $$TMPDIR; \
|
||||
# rm -f *.f *.o; \
|
||||
#
|
||||
# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
|
||||
# $(F77) $(FFLAGS) -c *.f; \
|
||||
#
|
||||
## rm *.f; \
|
||||
#
|
||||
# rm -f $@; \
|
||||
# ar rcv $@ *.o; \
|
||||
# ranlib $@; \
|
||||
##rm *.o; \
|
||||
#
|
||||
# cd $$BINDIR; \
|
||||
# rm -r $$TMPDIR
|
||||
|
||||
|
||||
|
||||
#.f.a:
|
||||
# $(F77) $(FFLAGS) -c $<
|
||||
# ar rcv $@ $*.o
|
||||
# ranlib $@
|
||||
# rm $*.o
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
nprogs: $(NPROGS)
|
||||
|
||||
xprogs: $(XPROGS)
|
||||
|
||||
lprogs: $(LPROGS)
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) *.a *.o *~
|
||||
|
||||
lint:
|
||||
lint -Q -Nn5000 -DNOSTRDUP $(INCLUDES) *.c
|
||||
|
||||
|
|
@ -162,7 +162,8 @@ C so tell the user
|
|||
JRECL=1
|
||||
OPEN(UNIT=IDEV,FILE=FILNAM,STATUS='OLD',
|
||||
+ READONLY,
|
||||
+ RECORDTYPE='STREAM',ERR=100)
|
||||
C + RECORDTYPE='STREAM',
|
||||
+ ERR=100)
|
||||
END IF
|
||||
IOK=0
|
||||
RETURN
|
||||
|
@ -669,6 +670,7 @@ C
|
|||
WRITE(*,*)'END IN GETRSL'
|
||||
END
|
||||
INTEGER FUNCTION SEEKRS(IDEV,IREC)
|
||||
INTEGER FSEEK
|
||||
EXTERNAL FSEEK
|
||||
C INTEGER FSEEK
|
||||
SEEKRS = FSEEK(IDEV,IREC,0)
|
||||
END
|
||||
|
|
|
@ -2,9 +2,10 @@
|
|||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <sys/types.h>
|
||||
#include "userface.h"
|
||||
#include "helpnmenu.h"
|
||||
|
||||
#include "FtoC.h" /* IMPORT: Fstr2Cstr and Cstr2Fstr */
|
||||
#include "helpnmenu.h"
|
||||
#include "userface.h"
|
||||
|
||||
/*
|
||||
* Prompts the user with either one yes/no question or another.
|
||||
|
@ -16,21 +17,21 @@
|
|||
* 1 = no
|
||||
* -1 = cancel
|
||||
*/
|
||||
int yesono(int choice, char *prompt1, char *prompt2) {
|
||||
int a;
|
||||
int yesono(int choice, char *prompt1, char *prompt2)
|
||||
{
|
||||
int a;
|
||||
|
||||
switch(choice) {
|
||||
case 0:
|
||||
return yesno(prompt1);
|
||||
case 1:
|
||||
a = yesno(prompt2);
|
||||
if (a>=0)
|
||||
a ^= 1;
|
||||
return a;
|
||||
default:
|
||||
fputs("yesno() called with bad 'choice'\n", stderr);
|
||||
return -1;
|
||||
}
|
||||
switch (choice) {
|
||||
case 0:
|
||||
return yesno(prompt1);
|
||||
case 1:
|
||||
a = yesno(prompt2);
|
||||
if (a >= 0) a ^= 1;
|
||||
return a;
|
||||
default:
|
||||
fputs("yesno() called with bad 'choice'\n", stderr);
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
/*--------------------------------------------------------------------------*\
|
||||
|
@ -41,51 +42,33 @@ int yesono(int choice, char *prompt1, char *prompt2) {
|
|||
|* *|
|
||||
\*--------------------------------------------------------------------------*/
|
||||
|
||||
void getint_x(int_f *MININ_p,
|
||||
int_f *MAXIN_p,
|
||||
int_f *DEF_p,
|
||||
char *PROMPT_p,
|
||||
int_f *VALUE_p, /* out: result */
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *IOK_p, /* out: status */
|
||||
int_fl PROMPT_l,
|
||||
int_fl HELPF_l)
|
||||
void getint_x(int_f *MININ_p, int_f *MAXIN_p, int_f *DEF_p, char *PROMPT_p,
|
||||
int_f *VALUE_p, /* out: result */
|
||||
int_f *KBIN_p, int_f *KBOUT_p, int_f *IHELPS_p, int_f *IHELPE_p,
|
||||
char *HELPF_p, int_f *IDEVH_p, int_f *IOK_p, /* out: status */
|
||||
int_fl PROMPT_l, int_fl HELPF_l)
|
||||
/*
|
||||
* Prompt for an integer in the range *MININ_p <= i <= *MAXIN_p
|
||||
* IOK=0 => OK
|
||||
* IOK=1 => Cancel
|
||||
*/
|
||||
{
|
||||
char prompt[256];
|
||||
int status;
|
||||
char prompt[256];
|
||||
int status;
|
||||
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
|
||||
*VALUE_p = getint((int)*MININ_p, (int)*MAXIN_p, (int)*DEF_p,
|
||||
prompt, &status);
|
||||
*IOK_p = (int_f)((status < 0)? 1:0);
|
||||
*VALUE_p =
|
||||
getint((int)*MININ_p, (int)*MAXIN_p, (int)*DEF_p, prompt, &status);
|
||||
*IOK_p = (int_f)((status < 0) ? 1 : 0);
|
||||
|
||||
return;
|
||||
return;
|
||||
}
|
||||
|
||||
void getrl_x(float *MININ_p,
|
||||
float *MAXIN_p,
|
||||
float *DEF_p,
|
||||
char *PROMPT_p,
|
||||
float *VALUE_p, /* out: result */
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *IOK_p,
|
||||
int_fl PROMPT_l,
|
||||
void getrl_x(float *MININ_p, float *MAXIN_p, float *DEF_p, char *PROMPT_p,
|
||||
float *VALUE_p, /* out: result */
|
||||
int_f *KBIN_p, int_f *KBOUT_p, int_f *IHELPS_p, int_f *IHELPE_p,
|
||||
char *HELPF_p, int_f *IDEVH_p, int_f *IOK_p, int_fl PROMPT_l,
|
||||
int_fl HELPF_l)
|
||||
/*
|
||||
* Prompt for a real in the range *MININ_p <= i <= *MAXIN_p
|
||||
|
@ -94,30 +77,21 @@ void getrl_x(float *MININ_p,
|
|||
* IOK=1 => Cancel
|
||||
*/
|
||||
{
|
||||
char prompt[256];
|
||||
int status;
|
||||
char prompt[256];
|
||||
int status;
|
||||
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
|
||||
*VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 2);
|
||||
*IOK_p = (int_f)((status < 0)? 1:0);
|
||||
*VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 2);
|
||||
*IOK_p = (int_f)((status < 0) ? 1 : 0);
|
||||
|
||||
return;
|
||||
return;
|
||||
}
|
||||
|
||||
void getrls_x(float *MININ_p,
|
||||
float *MAXIN_p,
|
||||
float *DEF_p,
|
||||
char *PROMPT_p,
|
||||
float *VALUE_p, /* out: result */
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *IOK_p,
|
||||
int_fl PROMPT_l,
|
||||
void getrls_x(float *MININ_p, float *MAXIN_p, float *DEF_p, char *PROMPT_p,
|
||||
float *VALUE_p, /* out: result */
|
||||
int_f *KBIN_p, int_f *KBOUT_p, int_f *IHELPS_p, int_f *IHELPE_p,
|
||||
char *HELPF_p, int_f *IDEVH_p, int_f *IOK_p, int_fl PROMPT_l,
|
||||
int_fl HELPF_l)
|
||||
/*
|
||||
* Prompt for a real in the range *MININ_p <= i <= *MAXIN_p
|
||||
|
@ -126,27 +100,20 @@ void getrls_x(float *MININ_p,
|
|||
* IOK=1 => Cancel
|
||||
*/
|
||||
{
|
||||
char prompt[256];
|
||||
int status;
|
||||
char prompt[256];
|
||||
int status;
|
||||
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
|
||||
*VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 10);
|
||||
*IOK_p = (int_f)((status < 0)? 1:0);
|
||||
*VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 10);
|
||||
*IOK_p = (int_f)((status < 0) ? 1 : 0);
|
||||
|
||||
return;
|
||||
return;
|
||||
}
|
||||
|
||||
void yesno_x(int_f *ANSWER_p,
|
||||
char *PROMPT_p,
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_fl PROMPT_l,
|
||||
int_fl HELPF_l)
|
||||
void yesno_x(int_f *ANSWER_p, char *PROMPT_p, int_f *IHELPS_p, int_f *IHELPE_p,
|
||||
char *HELPF_p, int_f *IDEVH_p, int_f *KBIN_p, int_f *KBOUT_p,
|
||||
int_fl PROMPT_l, int_fl HELPF_l)
|
||||
/*
|
||||
* Prompt the user with *PROMPT_l and get a YES or NO response.
|
||||
* ANSWER=-1 => Cancel
|
||||
|
@ -154,48 +121,35 @@ void yesno_x(int_f *ANSWER_p,
|
|||
* ANSWER=1 => NO
|
||||
*/
|
||||
{
|
||||
char prompt[256];
|
||||
char prompt[256];
|
||||
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
*ANSWER_p = (int_f)yesno(prompt);
|
||||
Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
|
||||
*ANSWER_p = (int_f)yesno(prompt);
|
||||
}
|
||||
|
||||
void yesono_x(int_f *CHOICE_p,
|
||||
char *P1_p,
|
||||
char *P2_p,
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_fl P1_l,
|
||||
int_fl P2_l,
|
||||
int_fl HELPF_l)
|
||||
void yesono_x(int_f *CHOICE_p, char *P1_p, char *P2_p, int_f *IHELPS_p,
|
||||
int_f *IHELPE_p, char *HELPF_p, int_f *IDEVH_p, int_f *KBIN_p,
|
||||
int_f *KBOUT_p, int_fl P1_l, int_fl P2_l, int_fl HELPF_l)
|
||||
/*
|
||||
* If CHOICE is 0, present a YESNO dialogue with prompt P1.
|
||||
* If CHOICE is 1, present a YESNO dialogue with prompt P2.
|
||||
*/
|
||||
{
|
||||
char prompt1[256], prompt2[256];
|
||||
char prompt1[256], prompt2[256];
|
||||
|
||||
Fstr2Cstr(P1_p, P1_l, prompt1, (int_fl)sizeof(prompt1));
|
||||
Fstr2Cstr(P2_p, P2_l, prompt2, (int_fl)sizeof(prompt2));
|
||||
Fstr2Cstr(P1_p, P1_l, prompt1, (int_fl)sizeof(prompt1));
|
||||
Fstr2Cstr(P2_p, P2_l, prompt2, (int_fl)sizeof(prompt2));
|
||||
|
||||
*CHOICE_p = (int_f)yesono(*CHOICE_p, prompt1, prompt2);
|
||||
*CHOICE_p = (int_f)yesono(*CHOICE_p, prompt1, prompt2);
|
||||
}
|
||||
|
||||
void gtstr_x(char *P_p, /* prompt */
|
||||
char *STRING_p, /* default value (if *LENGTH_p > 0) */
|
||||
char *NEW_p, /* out: dialogue result */
|
||||
void gtstr_x(char *P_p, /* prompt */
|
||||
char *STRING_p, /* default value (if *LENGTH_p > 0) */
|
||||
char *NEW_p, /* out: dialogue result */
|
||||
int_f *LENGTH_p, /* in: significant length of *STRING_p
|
||||
out: significant length of *NEW_p */
|
||||
int_f *KBOUT_p,
|
||||
int_f *KBIN_p,
|
||||
int_f *INFLAG_p, /* out: status */
|
||||
int_fl P_l,
|
||||
int_fl STRING_l,
|
||||
int_fl NEW_l)
|
||||
out: significant length of *NEW_p */
|
||||
int_f *KBOUT_p, int_f *KBIN_p, int_f *INFLAG_p, /* out: status */
|
||||
int_fl P_l, int_fl STRING_l, int_fl NEW_l)
|
||||
/*
|
||||
* Prompt with P for a string, default value STRING.
|
||||
* Return new string in NEW.
|
||||
|
@ -205,43 +159,43 @@ void gtstr_x(char *P_p, /* prompt */
|
|||
* INFLAG=3 => LENGTH=0 and NEW full of blanks (ie default)
|
||||
*/
|
||||
{
|
||||
char question[256], def[256];
|
||||
char *defptr;
|
||||
int ret;
|
||||
char question[256], def[256];
|
||||
char *defptr;
|
||||
int ret;
|
||||
|
||||
Fstr2Cstr(P_p, P_l, question, (int_fl)sizeof(question));
|
||||
if (*LENGTH_p > 0) {
|
||||
Fstr2Cstr(STRING_p, STRING_l, def, (int_fl)sizeof(def));
|
||||
defptr = def;
|
||||
} else
|
||||
defptr = 0;
|
||||
Fstr2Cstr(P_p, P_l, question, (int_fl)sizeof(question));
|
||||
if (*LENGTH_p > 0) {
|
||||
Fstr2Cstr(STRING_p, STRING_l, def, (int_fl)sizeof(def));
|
||||
defptr = def;
|
||||
}
|
||||
else
|
||||
defptr = 0;
|
||||
|
||||
ret = gtstr(question, defptr, NEW_p, (size_t)((NEW_l==1)?40:NEW_l));
|
||||
switch(ret) {
|
||||
case -1:
|
||||
*INFLAG_p = 2;
|
||||
*LENGTH_p = 1;
|
||||
return;
|
||||
case 0:
|
||||
*INFLAG_p = 0;
|
||||
*LENGTH_p = (int_f)strlen(NEW_p);
|
||||
Cstr2Fstr(NEW_p, NEW_p, NEW_l);
|
||||
return;
|
||||
case 1:
|
||||
*INFLAG_p = 3;
|
||||
*LENGTH_p = 0;
|
||||
}
|
||||
ret =
|
||||
gtstr(question, defptr, NEW_p, (size_t)((NEW_l == 1) ? 40 : NEW_l));
|
||||
switch (ret) {
|
||||
case -1:
|
||||
*INFLAG_p = 2;
|
||||
*LENGTH_p = 1;
|
||||
return;
|
||||
case 0:
|
||||
*INFLAG_p = 0;
|
||||
*LENGTH_p = (int_f)strlen(NEW_p);
|
||||
Cstr2Fstr(NEW_p, NEW_p, NEW_l);
|
||||
return;
|
||||
case 1:
|
||||
*INFLAG_p = 3;
|
||||
*LENGTH_p = 0;
|
||||
}
|
||||
}
|
||||
|
||||
void getstr_x(char *P_p, /* prompt */
|
||||
char *STRING_p, /* default value (if *LENGTH_p > 0) */
|
||||
char *NEW_p, /* out: dialogue result */
|
||||
void getstr_x(char *P_p, /* prompt */
|
||||
char *STRING_p, /* default value (if *LENGTH_p > 0) */
|
||||
char *NEW_p, /* out: dialogue result */
|
||||
int_f *MAXSTR_p, /* array length of *STRING_p and *NEW_p */
|
||||
int_f *LENGTH_p, /* in: significant length of *STRING_p
|
||||
out: significant length of *NEW_p */
|
||||
int_f *KBOUT_p,
|
||||
int_f *KBIN_p,
|
||||
int_f *INFLAG_p, /* out: status */
|
||||
int_f *KBOUT_p, int_f *KBIN_p, int_f *INFLAG_p, /* out: status */
|
||||
int_fl P_l)
|
||||
/*
|
||||
* Present a dialogue requesting a string result with the given prompt
|
||||
|
@ -252,31 +206,16 @@ void getstr_x(char *P_p, /* prompt */
|
|||
* given *STRING_p and *NEW_p.
|
||||
*/
|
||||
{
|
||||
gtstr_x(P_p,
|
||||
STRING_p,
|
||||
NEW_p,
|
||||
LENGTH_p,
|
||||
KBOUT_p,
|
||||
KBIN_p,
|
||||
INFLAG_p,
|
||||
P_l,
|
||||
*MAXSTR_p,
|
||||
*MAXSTR_p);
|
||||
gtstr_x(P_p, STRING_p, NEW_p, LENGTH_p, KBOUT_p, KBIN_p, INFLAG_p, P_l,
|
||||
*MAXSTR_p, *MAXSTR_p);
|
||||
}
|
||||
|
||||
void radion_x(char *TITLE_p,
|
||||
char *PROMPT_p, /* Actually: *PROMPT_p[*NB_p] */
|
||||
int_f *NB_p, /* Number of buttons (1..NB) */
|
||||
int_f *CHOICE_p, /* in: default button
|
||||
out: selected button */
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_fl TITLE_l,
|
||||
int_fl PROMPT_l,
|
||||
void radion_x(char *TITLE_p, char *PROMPT_p, /* Actually: *PROMPT_p[*NB_p] */
|
||||
int_f *NB_p, /* Number of buttons (1..NB) */
|
||||
int_f *CHOICE_p, /* in: default button
|
||||
out: selected button */
|
||||
int_f *IHELPS_p, int_f *IHELPE_p, char *HELPF_p, int_f *IDEVH_p,
|
||||
int_f *KBIN_p, int_f *KBOUT_p, int_fl TITLE_l, int_fl PROMPT_l,
|
||||
int_fl HELPF_l)
|
||||
/*
|
||||
* Present a ``radio button'' dialogue allowing the user to select
|
||||
|
@ -286,37 +225,32 @@ void radion_x(char *TITLE_p,
|
|||
* CHOICE=-1 => Cancel
|
||||
*/
|
||||
{
|
||||
char **opt, title[256];
|
||||
int i, numopts = (int)*NB_p;
|
||||
char **opt, title[256];
|
||||
int i, numopts = (int)*NB_p;
|
||||
|
||||
/* initialise options array */
|
||||
opt = (char **)malloc(numopts * sizeof(char *));
|
||||
opt[0] = (char *)malloc((unsigned int)((PROMPT_l+1) * numopts));
|
||||
for (i=0; i<numopts; i++) {
|
||||
opt[i] = opt[0] + (PROMPT_l+1)*i;
|
||||
Fstr2Cstr(PROMPT_p+(i*PROMPT_l), PROMPT_l, opt[i], PROMPT_l+1);
|
||||
}
|
||||
/* initialise options array */
|
||||
opt = (char **)malloc(numopts * sizeof(char *));
|
||||
opt[0] = (char *)malloc((unsigned int)((PROMPT_l + 1) * numopts));
|
||||
for (i = 0; i < numopts; i++) {
|
||||
opt[i] = opt[0] + (PROMPT_l + 1) * i;
|
||||
Fstr2Cstr(PROMPT_p + (i * PROMPT_l), PROMPT_l, opt[i],
|
||||
PROMPT_l + 1);
|
||||
}
|
||||
|
||||
Fstr2Cstr(TITLE_p, TITLE_l, title, (int_fl)sizeof(title));
|
||||
Fstr2Cstr(TITLE_p, TITLE_l, title, (int_fl)sizeof(title));
|
||||
|
||||
*CHOICE_p = (int_f)radion(title, opt, *NB_p, *CHOICE_p);
|
||||
|
||||
free((void *)opt[0]);
|
||||
free((void *)opt);
|
||||
return;
|
||||
*CHOICE_p = (int_f)radion(title, opt, *NB_p, *CHOICE_p);
|
||||
|
||||
free((void *)opt[0]);
|
||||
free((void *)opt);
|
||||
return;
|
||||
}
|
||||
|
||||
void check4_x(char *P1_p, char *P2_p, char *P3_p, char *P4_p,
|
||||
int_f *C1_p, int_f *C2_p, int_f *C3_p, int_f *C4_p,
|
||||
int_f *IHELPS_p,
|
||||
int_f *IHELPE_p,
|
||||
char *HELPF_p,
|
||||
int_f *IDEVH_p,
|
||||
int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_f *IOK_p,
|
||||
int_fl P1_l, int_fl P2_l, int_fl P3_l, int_fl P4_l,
|
||||
int_fl HELPF_l)
|
||||
void check4_x(char *P1_p, char *P2_p, char *P3_p, char *P4_p, int_f *C1_p,
|
||||
int_f *C2_p, int_f *C3_p, int_f *C4_p, int_f *IHELPS_p,
|
||||
int_f *IHELPE_p, char *HELPF_p, int_f *IDEVH_p, int_f *KBIN_p,
|
||||
int_f *KBOUT_p, int_f *IOK_p, int_fl P1_l, int_fl P2_l,
|
||||
int_fl P3_l, int_fl P4_l, int_fl HELPF_l)
|
||||
/*
|
||||
* Present a ``checkbox'' dialogue allowing the user to alter the
|
||||
* Boolean state of four items.
|
||||
|
@ -326,25 +260,28 @@ void check4_x(char *P1_p, char *P2_p, char *P3_p, char *P4_p,
|
|||
* IOK=1 => Cancel
|
||||
*/
|
||||
{
|
||||
int ret;
|
||||
char *prompts[4];
|
||||
int *bools[4];
|
||||
int ret;
|
||||
char *prompts[4];
|
||||
int *bools[4];
|
||||
|
||||
prompts[0] = P1_p; bools[0] = (int *)C1_p;
|
||||
prompts[1] = P2_p; bools[1] = (int *)C2_p;
|
||||
prompts[2] = P3_p; bools[2] = (int *)C3_p;
|
||||
prompts[3] = P4_p; bools[3] = (int *)C4_p;
|
||||
prompts[0] = P1_p;
|
||||
bools[0] = (int *)C1_p;
|
||||
prompts[1] = P2_p;
|
||||
bools[1] = (int *)C2_p;
|
||||
prompts[2] = P3_p;
|
||||
bools[2] = (int *)C3_p;
|
||||
prompts[3] = P4_p;
|
||||
bools[3] = (int *)C4_p;
|
||||
|
||||
ret = checkn(4, prompts, bools);
|
||||
ret = checkn(4, prompts, bools);
|
||||
|
||||
if (ret == 0)
|
||||
*IOK_p = 0;
|
||||
else
|
||||
*IOK_p = 1;
|
||||
if (ret == 0)
|
||||
*IOK_p = 0;
|
||||
else
|
||||
*IOK_p = 1;
|
||||
}
|
||||
|
||||
void getopt_x(int_f *KBIN_p,
|
||||
int_f *KOPT_p,
|
||||
void getopt_x(int_f *KBIN_p, int_f *KOPT_p,
|
||||
int_f *IOPT_p) /* out: option number selected */
|
||||
/*
|
||||
* Select a function to execute
|
||||
|
@ -353,58 +290,51 @@ void getopt_x(int_f *KBIN_p,
|
|||
* KOPT=3 => menu option requested
|
||||
*/
|
||||
{
|
||||
*IOPT_p = (int_f)getcopt((int *)KOPT_p);
|
||||
switch(*KOPT_p) {
|
||||
case -3:
|
||||
case -2:
|
||||
*KOPT_p = 0;
|
||||
*IOPT_p = 2;
|
||||
break;
|
||||
case -1:
|
||||
*KOPT_p = 0;
|
||||
*IOPT_p = 1;
|
||||
break;
|
||||
}
|
||||
*IOPT_p = (int_f)getcopt((int *)KOPT_p);
|
||||
switch (*KOPT_p) {
|
||||
case -3:
|
||||
case -2:
|
||||
*KOPT_p = 0;
|
||||
*IOPT_p = 2;
|
||||
break;
|
||||
case -1:
|
||||
*KOPT_p = 0;
|
||||
*IOPT_p = 1;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
void showfi_x(int_f *KBOUT_p,
|
||||
char *STRING_p,
|
||||
int_fl STRING_l)
|
||||
void showfi_x(int_f *KBOUT_p, char *STRING_p, int_fl STRING_l)
|
||||
/*
|
||||
* Display `STRING', the name of the current file(s).
|
||||
*/
|
||||
{
|
||||
char func[256];
|
||||
char func[256];
|
||||
|
||||
Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
|
||||
showfi(func);
|
||||
Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
|
||||
showfi(func);
|
||||
}
|
||||
|
||||
|
||||
void showfu_x(int_f *KBOUT_p,
|
||||
char *STRING_p,
|
||||
int_fl STRING_l)
|
||||
void showfu_x(int_f *KBOUT_p, char *STRING_p, int_fl STRING_l)
|
||||
/*
|
||||
* Display `STRING', the name of the current function.
|
||||
*/
|
||||
{
|
||||
char func[256];
|
||||
char func[256];
|
||||
|
||||
Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
|
||||
showfu(func);
|
||||
Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
|
||||
showfu(func);
|
||||
}
|
||||
|
||||
void errom_x(int_f *KBOUT_p,
|
||||
char *STRING_p,
|
||||
int_fl STRING_l)
|
||||
void errom_x(int_f *KBOUT_p, char *STRING_p, int_fl STRING_l)
|
||||
/*
|
||||
* Display the error message `STRING'.
|
||||
*/
|
||||
{
|
||||
char err[256];
|
||||
char err[256];
|
||||
|
||||
Fstr2Cstr(STRING_p, STRING_l, err, (int_fl)sizeof(err));
|
||||
errom(err);
|
||||
Fstr2Cstr(STRING_p, STRING_l, err, (int_fl)sizeof(err));
|
||||
errom(err);
|
||||
}
|
||||
|
||||
void busy_x(int_f *KBOUT_p)
|
||||
|
@ -413,7 +343,7 @@ void busy_x(int_f *KBOUT_p)
|
|||
* next dialogue function is called.
|
||||
*/
|
||||
{
|
||||
busy();
|
||||
busy();
|
||||
}
|
||||
|
||||
/*
|
||||
|
@ -421,10 +351,8 @@ void busy_x(int_f *KBOUT_p)
|
|||
* 0 for ok
|
||||
* -1 for cancel
|
||||
*/
|
||||
void bpause_x(int_f *KBIN_p,
|
||||
int_f *KBOUT_p,
|
||||
int_f *IOK_p) {
|
||||
|
||||
*IOK_p = (int_f)bpause();
|
||||
void bpause_x(int_f *KBIN_p, int_f *KBOUT_p, int_f *IOK_p)
|
||||
{
|
||||
*IOK_p = (int_f)bpause();
|
||||
}
|
||||
|
||||
|
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -1,5 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
||||
|
@ -44,38 +42,35 @@
|
|||
|
||||
/* define any special resource names here that are not in <X11/StringDefs.h> */
|
||||
|
||||
#define XtNgraphResource "graphResource"
|
||||
#define XtCGraphResource "GraphResource"
|
||||
|
||||
#define XtNdimBackground "dimBackground"
|
||||
#define XtNexposeCallback "exposeCallback"
|
||||
#define XtNgraphColour1 "graphColour1"
|
||||
#define XtNgraphColour2 "graphColour2"
|
||||
#define XtNgraphColour3 "graphColour3"
|
||||
#define XtNgraphColour4 "graphColour4"
|
||||
#define XtNresizeCallback "resizeCallback"
|
||||
#define XtNgraphResource "graphResource"
|
||||
#define XtCGraphResource "GraphResource"
|
||||
|
||||
#define XtNdimBackground "dimBackground"
|
||||
#define XtNexposeCallback "exposeCallback"
|
||||
#define XtNgraphColour1 "graphColour1"
|
||||
#define XtNgraphColour2 "graphColour2"
|
||||
#define XtNgraphColour3 "graphColour3"
|
||||
#define XtNgraphColour4 "graphColour4"
|
||||
#define XtNresizeCallback "resizeCallback"
|
||||
|
||||
/* declare specific GraphWidget class and instance datatypes */
|
||||
|
||||
typedef struct _GraphClassRec *GraphWidgetClass;
|
||||
typedef struct _GraphRec *GraphWidget;
|
||||
|
||||
typedef struct _GraphClassRec *GraphWidgetClass;
|
||||
typedef struct _GraphRec *GraphWidget;
|
||||
|
||||
/* declare the class constant */
|
||||
|
||||
extern WidgetClass graphWidgetClass;
|
||||
|
||||
|
||||
/* ---- Exported procedures ---- */
|
||||
|
||||
extern Pixel GraphColour1(Widget w);
|
||||
extern Pixel GraphColour2(Widget w);
|
||||
extern Pixel GraphColour3(Widget w);
|
||||
extern Pixel GraphColour4(Widget w);
|
||||
extern GC GraphGC1(Widget w);
|
||||
extern GC GraphGC2(Widget w);
|
||||
extern GC GraphGC3(Widget w);
|
||||
extern GC GraphGC4(Widget w);
|
||||
extern GC GraphGC1(Widget w);
|
||||
extern GC GraphGC2(Widget w);
|
||||
extern GC GraphGC3(Widget w);
|
||||
extern GC GraphGC4(Widget w);
|
||||
|
||||
#endif /* _Graph_h */
|
||||
|
|
|
@ -1,4 +1,3 @@
|
|||
#include <X11/copyright.h>
|
||||
|
||||
/* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
|
||||
/* Copyright Massachusetts Institute of Technology 1987, 1988 */
|
||||
|
|
|
@ -0,0 +1,90 @@
|
|||
#
|
||||
# Makefile for ted (trace editor) - Alpha fork
|
||||
#
|
||||
|
||||
#
|
||||
#Turning on the AUTO_CLIP switch allows ted to automatically
|
||||
#select a left (using the -enzyme option or the .enzyme in the
|
||||
#Xted file) and right cutoff on your sequence (using 2 out of
|
||||
#5 N's)
|
||||
#
|
||||
# Turning on the SAVE_EDITS switch allows the user to maintain
|
||||
# copies of their edits, i.e. when you open up ted on a file
|
||||
# that you have already edited, the old edits show up in the
|
||||
# ted edit window. The user may also call up any of their
|
||||
# past editing sessions.
|
||||
#
|
||||
#Turning on the DEF_OUT switch makes
|
||||
# trace_name.seq the default output file name
|
||||
#
|
||||
#SWITCHES = -DAUTO_CLIP -DDEF_OUT -DSAVE_EDITS
|
||||
SWITCHES = -DAUTO_CLIP
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = ted
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
|
||||
#
|
||||
# Compiler - debug on
|
||||
#
|
||||
CC= gfortran
|
||||
INCLUDES = -I$(SRC)
|
||||
CFLAGS= -g $(SWITCHES) $(INCLUDES)
|
||||
LIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#-ldnet_stub
|
||||
#
|
||||
LD= gfortran
|
||||
LDFLAGS= -g
|
||||
|
||||
#
|
||||
# Object files
|
||||
#
|
||||
TEDOBJS=\
|
||||
ted.o\
|
||||
dialogues.o\
|
||||
seq.o\
|
||||
seqIOPlain.o\
|
||||
seqIOABI.o\
|
||||
help.o\
|
||||
display.o\
|
||||
traceDisplay.o\
|
||||
basesDisplay.o\
|
||||
Graph.o\
|
||||
seqIOEdit.o\
|
||||
seqIOALF.o\
|
||||
seqIOSCF.o\
|
||||
seqOutput.o\
|
||||
opp.o\
|
||||
info.o\
|
||||
fpoint.o\
|
||||
mach-io.o\
|
||||
seqRead.o
|
||||
|
||||
|
||||
#
|
||||
# Linking
|
||||
#
|
||||
ted: $(TEDOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o : $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
clean:
|
||||
rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
|
||||
|
||||
all: $(PROGS)
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
#
|
||||
# Makefile for subclonedb
|
||||
#
|
||||
|
||||
#
|
||||
# Programs made by this makefile
|
||||
#
|
||||
PROGS = update_subclones
|
||||
|
||||
#
|
||||
# Where the wild things are
|
||||
#
|
||||
SRC = .
|
||||
MISCSRC = $(SRC)/../Misc
|
||||
MISCBIN = $(MISCSRC)
|
||||
INCLUDES = -I$(SRC) -I$(MISCSRC)
|
||||
|
||||
#
|
||||
# Alpha
|
||||
#
|
||||
CC = cc
|
||||
CFLAGS = -g $(INCLUDES)
|
||||
LD = cc
|
||||
LDFLAGS = -g
|
||||
|
||||
#
|
||||
# Here they are
|
||||
#
|
||||
|
||||
update_subclones : update_subclones.o $(MISCBIN)/misc.a
|
||||
$(LD) $(LDFLAGS) -o update_subclones update_subclones.o $(MISCBIN)/misc.a
|
||||
|
||||
#
|
||||
# Special dependencies
|
||||
#
|
||||
all: $(PROGS)
|
||||
|
||||
clean:
|
||||
/bin/rm -f $(PROGS)
|
||||
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
|
@ -0,0 +1,137 @@
|
|||
# Makefile for vepe - Alpha version
|
||||
# -------------------------------
|
||||
|
||||
PROGS= vepe
|
||||
|
||||
all: $(PROGS)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#
|
||||
# ``Interesting'' suffices that make needs to know about
|
||||
#
|
||||
.SUFFIXES: .a $(SUFFIXES)
|
||||
|
||||
|
||||
#
|
||||
# Directories
|
||||
#
|
||||
SRC = .
|
||||
#STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden
|
||||
STADENSRC=$(SRC)/../staden
|
||||
STADENBIN=$(STADENSRC)
|
||||
# Use the ted sources compiled for staden executables
|
||||
INCLUDES= -I$(STADENSRC)
|
||||
|
||||
|
||||
#
|
||||
# Compilers and flags
|
||||
#
|
||||
# debug on
|
||||
CC= cc
|
||||
CFLAGS= -g $(INCLUDES)
|
||||
F77= gfortran
|
||||
FFLAGS= -g
|
||||
LD= gfortran
|
||||
LDFLAGS= -g
|
||||
|
||||
FLAGS = -lutil -lm
|
||||
#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
|
||||
XLIBS= -lXaw -lXt -lXmu -lXext -lX11
|
||||
#LFLAGS= $(FLIBS)
|
||||
XLFLAGS= $(FLIBS) $(XLIBS)
|
||||
|
||||
#
|
||||
# Avoid compilation of objects in remote directories
|
||||
#
|
||||
$(STADENBIN)/%.o : $(STADENSRC)/%.f
|
||||
$(STADENBIN)/%.o : $(STADENSRC)/%.c
|
||||
|
||||
#
|
||||
# Common objects, needed by every program
|
||||
#
|
||||
COMMONOBJS=\
|
||||
$(STADENBIN)/seeme-aix.o\
|
||||
$(STADENBIN)/nxspec.o\
|
||||
$(STADENBIN)/userface.o\
|
||||
$(STADENBIN)/userfacecom.o\
|
||||
$(STADENBIN)/helpnmenu.o\
|
||||
$(STADENBIN)/nxhelpmenu.o\
|
||||
$(STADENBIN)/FtoC.o\
|
||||
$(STADENBIN)/subs89.a\
|
||||
|
||||
|
||||
#
|
||||
# Building the programs
|
||||
# This should be just a linking phase because all of the object
|
||||
# files and library files are generated using implicit rules.
|
||||
# We use the fortran compiler to do linking.
|
||||
#
|
||||
|
||||
#
|
||||
# Vector excision program
|
||||
#
|
||||
|
||||
VEP=\
|
||||
vep.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
$(STADENBIN)/subs89.a
|
||||
|
||||
|
||||
VEPOBJS=\
|
||||
$(VEP)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
|
||||
vep: $(VEPOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(VEPOBJS) $(LFLAGS)
|
||||
|
||||
|
||||
|
||||
VEPE=\
|
||||
vepe.o\
|
||||
$(STADENBIN)/dias89.a\
|
||||
expio.o\
|
||||
expFileIO.o
|
||||
|
||||
|
||||
VEPEOBJS=\
|
||||
$(VEPE)\
|
||||
$(COMMONOBJS)
|
||||
|
||||
|
||||
vepe: $(VEPEOBJS)
|
||||
$(LD) $(LDFLAGS) -o $@ $(VEPEOBJS) $(LFLAGS)
|
||||
|
||||
COBJS = expFileIO.o testc.o
|
||||
FOBJS = expFileIO.o testf.o
|
||||
|
||||
|
||||
testc: $(COBJS)
|
||||
$(CC) $(CFLAGS) -o $@ $(COBJS)
|
||||
|
||||
testf: $(FOBJS)
|
||||
$(F77) $(FFLAGS) -o $@ $(FOBJS)
|
||||
|
||||
|
||||
#
|
||||
# Files requiring simple C compilation (thing.c -> thing.o)
|
||||
#
|
||||
%.o: %.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
%.o: $(SRC)/%.c
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
|
||||
#
|
||||
# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
|
||||
#
|
||||
%.o: $(SRC)/%.f
|
||||
$(F77) $(FFLAGS) -c $<
|
||||
|
||||
clean:
|
||||
rm -f $(PROGS) *.o *.a *~
|
||||
|
||||
|
||||
install: clean all
|