#!/bin/bash # error message function err() { echo echo "********************************* ERROR ***********************" 1>&2 echo "`basename $0`: $@" 1>&2 echo "***************************** END OF ERROR ********************" 1>&2 echo " Please rerun script !!!" 1>&2 exit 1 } cont() { echo "Warning: $@" 1>&2 echo 'Do you want to continue [y]' read var case "$var" in n) err "Script aborted by user" ;; *) echo 'Continuing...' ;; esac } untar() { #remove old DEPOT BUG rm -f DEPOT/gde/bin if [ ! -x $cwd/zcat ]; then if chmod 755 $cwd/zcat; then echo ">>> chmod 755 $cwd/zcat succesfull" else err "Cannot chmod of $cwd/zcat" fi fi if [ ! -r $cwd/$1 ]; then err "Cannot find or read file $cwd/$1" fi if $cwd/zcat $cwd/$1 |tar xfv -; then echo ">>> $1 uncompressed and untared" else err "Error in uncompressing or untaring $1" fi } seperator() { echo '' echo ' *******************************************' } seperator echo 'Welcome to the ARB Package' seperator echo ' Note: - You may abort this script with ctrl-"C"' echo ' - You can rerun this script as often as you like' echo ' - Old ARB data will be kept if requested (in this case' echo ' you can simply change some options)' echo ' - Pressing will select the value in brackets' seperator echo 'Please answer some questions:' seperator echo 'Enter path where to install ARB ?' echo ' ARB is not a single programm but a set of programs, datafiles ...' echo ' To install ARB correctly all files are stored in a single ' echo ' directory. This script creates such a directory and copies all' echo ' data into it, sets the correct permissions and optionally installs' echo ' some X11 stuff. Please enter the path of the directory where you want' echo ' to install ARB.' echo ' Notes: This script optionally creates the destination directory.' echo ' You should have write permission at the destination location.' echo ' - To install ARB in your home directory: Enter "arb"' echo ' - Otherwise become root and rerun script.' echo ' - On Linux computers this script should be run under root' echo '' echo ' Example: If there is enough space (~50 MB) at your /usr partition and' echo ' you want to install arb at /usr/arb, enter "/usr/arb"' if [ "$ARBHOME" != "" ]; then if test -f $ARBHOME/lib/arb_tcp.dat; then echo " Note: I found an old arb program at $ARBHOME" fi fi echo "Enter full installation path: [${ARBHOME:-/usr/arb}]" read ARBHOMEI echo echo if [ "$ARBHOMEI" = "" ]; then ARBHOME="${ARBHOME:-/usr/arb}"; else ARBHOME="${ARBHOMEI}"; fi cwd=`pwd` if test -d $ARBHOME; then echo 'Creating backup copy of arb_tcp.dat ..' cp $ARBHOME/lib/arb_tcp.dat arb_tcp_`date +%Y%m%d`.dat if test -w $ARBHOME; then seperator echo 'The destination directory' echo " $ARBHOME" echo 'already exists!' echo ' You can delete the old directory before installing ARB' echo ' or only update/change options of the old version.' echo 'Delete old directory (y/n)[n]?' read delete_dir echo case "$delete_dir" in y) if rm -r $ARBHOME/* ;then echo ">>> all data in $ARBHOME deleted" else cont "cannot delete all data in $ARBHOME" fi;; *) if test -f $ARBHOME/lib/arb_tcp.dat; then bckup=$ARBHOME/lib/arb_tcp.dat.`date +%y%m%d%H%M%S` echo ">>>old $ARBHOME/lib/arb_tcp.dat found" echo ">>>backup to $bckup" cp $ARBHOME/lib/arb_tcp.dat $bckup fi echo ">>> old data not deleted";; esac else err "directory exists and is not writable"; fi else if mkdir -p $ARBHOME; then echo ">>> $ARBHOME created" else err "cannot create directory $ARBHOME"; fi fi cd $ARBHOME ARBHOME=`pwd` if test -d lib/pictures; then seperator echo "Old ARB package found (type n to change only some options)." echo " Do you want to update the old package: (y/n)[y]" read var; case "$var" in n) echo "Old version unchanged";; *) echo "updating ARB"; untar arb.tgz;; esac else untar arb.tgz; fi if test -f $cwd/arb_ale.tgz; then if test -f DEPOT2/emacs; then seperator echo "Old ARB_ALE package found" echo "ARB_ALE is a sophisticated alignment editor written by RDP" echo " Do you want to update the old package: (y/n)[y]" read var; case "$var" in n) echo "Old ARB_ALE version unchanged";; *) echo "updating ARB_ALE" untar arb_ale.tgz;; esac else untar arb_ale.tgz; fi fi seperator echo 'Specify PT_SERVER files location' echo ' ARB needs a writeable directory to store the pt_server files. ' echo ' Those files are needed for fast database search' echo ' (by probe_design, probe_match and the automatic aligner)' echo ' and need a lot of disc space (up to several 100 mega bytes,' echo ' e.g. 4000 16S RNA sequences require about 40 MB).' echo ' This files are not created now. They can be build by any user via' echo ' ' echo ' You may define a special directory as the pt_server files location.' echo ' This prevents any loss of data installing a new version of ' echo ' ARB. ' echo 'Where do you want to put your pt_server data' echo ' 1. - (new installation of ARB)' echo ' for placing pt_server data within ARB directory tree' echo ' (Default location).' echo ' - (updating ARB)' echo ' using the previous location' echo ' 2. "Path" to link pt_server data directory to' echo " (if you choose this option you won't loose your PT-Servers when doing future software updates)" echo 'Enter path:' read pt_dir echo case "$pt_dir" in "") echo "installing the pt_server data in $ARBHOME/lib/pts" if test -h ${ARBHOME}/lib/pts ; then echo "Are you sure to delete " echo ">>> pt_server files at non default location:" ls -ld ${ARBHOME}/lib/pts else if test -d ${ARBHOME}/lib/pts; then echo ">>> pt_server files at default location: unchanged" else (cd lib;rm -f pts;mkdir pts;) fi fi;; *) echo "changing your pt_server file location" if test -h ${ARBHOME}/lib/pts; then echo ">>> non default location found: removing old link" rm lib/pts else if test -d ${ARBHOME}/lib/pts; then echo ">>> data in default location found" echo 'Do you want to remove old ptserver data (recommended)? [y]' read ANSWER case "$ANSWER" in n) echo 'data not deleted' ;; *) rm -r lib/pts echo 'data deleted' ;; esac fi fi if test ! -d $pt_dir; then echo ">>> Creating special PT_SERVER directory $pt_dir" if mkdir -p $pt_dir; then echo ">>> $pt_dir created" else err "Couldn't create $pt_dir" fi fi (cd lib;ln -s $pt_dir pts;) esac seperator echo 'Who is responsible for the PT_SERVER index files ?' echo ' Answer y: if you trust your users (less administration)' echo ' n: if YOU want to administrate all PT_SERVER files' echo ' or simply press return to keep the settings of an old installation.' echo 'Should everybody be allowed to build/update PT_SERVER files (y/n/dont_change)[dont_change]?' read var echo case "$var" in y) echo ">>> all users are allowed to update the PT_SERVER"; chmod 777 lib/pts chmod 666 lib/pts/* 2>/dev/null ;; n) echo ">>> only `whoami` is allowed to update the pt_server"; chmod 755 lib/pts chmod 644 lib/pts/* 2>/dev/null ;; *) echo ">>> flags unchanged";; esac seperator echo 'NameServer installation' echo ' The NameServer is a programm, that synchronizes all species names' echo ' of the databases of different users.' echo ' Users that import foreign data into their database and want to' echo ' export those data to other ARB users should be allowed to change' echo ' the names file in $ARBHOME/lib/nas/names.dat' echo ' Answer y: if all users may import foreign databases' echo ' n: if there are some mean untrusty users' echo ' or simply press return to keep the old settings' echo 'Do you trust your users (y/n/dont_change)[dont_change]?' read var echo case "$var" in y) echo ">>> all user are allowed to change the names file"; chmod 777 lib/nas chmod 666 lib/nas/*;; n) echo ">>> only `whoami` is allowed to change the names file ${ARBHOME}/lib/nas/names.dat" chmod 755 lib/nas chmod 644 lib/nas/*;; *) echo ">>> flags unchanged";; esac seperator echo 'Networking' echo ' To speed up calculation one special host can be assigned as' echo ' the PT_SERVER host. That means that all database search is done' echo ' on that host. This saves computer resources as different users' echo ' may share one server.' echo ' To get the best results this host "H" should:' echo ' 1. be fast,' echo ' 2. have a lot of real memory (>=64 meg),' echo ' 3. have a lot of swap space (>=400 meg),' echo ' 4. allow all users to run "ssh H ...",' echo ' 5. contain the discs with the PT_SERVER files.' echo ' n You want to assign a special Network host' echo ' s You have a Stand alone computer' if test "X$bckup" != "X"; then echo ' o Use information of already installed ARB' echo 'Choose (s/n/o)[s]?' else echo 'Choose (s/n)[s]?' fi read var echo case "$var" in o) mv $bckup lib/arb_tcp.dat; echo ">>> old lib/arb_tcp.dat restored";; n) seperator echo "Enter the name of your host for the pt_server" read host echo "Checking connection to $host" if ssh $host ls >/dev/zero; then echo ">>> ssh $host ok" else err ">>> cannot run 'ssh $host'"; fi rm -f lib/arb_tcp.dat; cat lib/arb_tcp_org.dat |sed -e "/localhost\:/$host\:/g" >lib/arb_tcp.dat echo ">>> server installed";; *) cp lib/arb_tcp_org.dat lib/arb_tcp.dat echo ">>> server installed";; esac # install missing libraries seperator ( export ARBHOME ; $ARBHOME/lib/addlibs/install_libs.sh ) seperator echo ">>> Installation Complete" seperator SHELL_ANS=0 while [ "$SHELL_ANS" = "0" ]; do echo "Finally, you have to tell your system where to find arb." echo "First find out which shell you are using, by opening a shell and typing" echo ' echo $shell' echo "" echo "Depending on what is your shell there are three choices:" echo "" echo " 1. Change your local .profile or .bashrc (if you are using ksh/bash, which" echo " is the default shell for Linux)" echo " 2. Change your local .cshrc file (if you are using csh/tcsh)" echo " 3. Create an alias for arb (any shell)" echo "" echo "Enter (1,2 or 3) to achieve further installation instructions:" read var echo ''; echo '**********************************************************************************************'; echo 'Follow the steps below with care!!!'; echo ''; case "$var" in 1) echo '******************************************************'; echo "add the following lines to your ~/.profile"; echo "or to your ~/.bashrc for bash-users"; echo '******************************************************'; echo " ARBHOME=$ARBHOME;export ARBHOME"; echo ' LD_LIBRARY_PATH=${ARBHOME}/lib:${LD_LIBRARY_PATH}'; echo ' export LD_LIBRARY_PATH'; echo ' PATH=${ARBHOME}/bin:${PATH}'; echo ' export PATH'; echo ' ' echo 'enter the following command:'; echo ' . ~/.profile' SHELL_ANS=1 ;; 2) echo '******************************************'; echo "add the following lines to your ~/.cshrc"; echo '******************************************'; echo " setenv ARBHOME $ARBHOME"; if test "X${LD_LIBRARY_PATH}" != "X"; then echo ' setenv LD_LIBRARY_PATH $ARBHOME/lib\:$LD_LIBRARY_PATH'; else echo ' setenv LD_LIBRARY_PATH $ARBHOME/lib'; fi echo ' setenv PATH $ARBHOME/bin\:$PATH'; echo ' ' echo 'enter the following command:'; echo ' source ~/.cshrc' SHELL_ANS=1 ;; 3) echo '**************************************************'; echo "add one of the following lines to your init file"; echo '**************************************************'; echo "# bash users add to ~/.bashrc:"; echo " alias arb=$ARBHOME/bin/arb"; echo "# tcsh users add to ~/.cshrc:"; echo " alias arb '$ARBHOME/bin/arb'"; SHELL_ANS=1 ;; *) echo 'Wrong answer';; esac done echo "" echo "Note for sysadmins:" echo " In order to provide arb for all users," echo " edit the global shell init file(s) in /etc" echo " (/etc/bash.bashrc, /etc/csh.cshrc or similar)" echo " in the same manner as described above for the" echo " local shell init files." echo "" echo "When you performed these changes, open a new terminal window" echo "and start arb by typing" echo "" echo " arb" echo "" echo "Have much fun using ARB" echo "ARB Team " echo "" unset host unset cwd unset ARBHOME unset delete_dir unset keep_debug unset pt_dir unset var