Compare commits
2 commits
e43f849064
...
047d935b02
| Author | SHA1 | Date | |
|---|---|---|---|
| 047d935b02 | |||
| a8136c75ba |
7 changed files with 67 additions and 2265 deletions
67
README.md
Normal file
67
README.md
Normal file
|
|
@ -0,0 +1,67 @@
|
|||
# STADEN-LG
|
||||
|
||||
STADEN Last Generation
|
||||
|
||||
## Introduction
|
||||
|
||||
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
|
||||
|
||||
Loading…
Reference in a new issue