#!/bin/bash # error message function (nested exit): trap "exit 1" TERM export ARBINST_SCRIPT_PID=$$ err() { echo "Error in `basename $0`:" 1>&2 echo " $@" 1>&2 echo "Please fix and then rerun script!" 1>&2 kill -s TERM $ARBINST_SCRIPT_PID } separator() { echo '' echo ' *******************************************' } separator echo 'Welcome to the ARB Package' test -z "${BASH_VERSINFO}" && separator && err "Please call this script using 'bash arb_install.sh'" elim_invalid_chars() { local FILE="${1}" # remove some characters really unwanted in paths: FILE=${FILE// /} FILE=${FILE//\'/} FILE=${FILE//\"/} FILE=${FILE//\`/} echo ${FILE} } DL_DIR=$(pwd) DL_NS=$(elim_invalid_chars "${DL_DIR}") if [ ! "$DL_NS" = "$DL_DIR" ]; then separator if [ ! "$DL_NS" = "" ]; then echo "Note: the path '$DL_NS' would be ok.." fi err "Your download directory '$DL_DIR' contains invalid characters." fi 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 [ ! -r $cwd/$1 ]; then err "Cannot find or read file $cwd/$1" fi if gunzip --stdout $cwd/$1 | tar xfv -; then echo ">>> $1 uncompressed and untared" if [ ! -e bin/arb_ntree ]; then err "bin/arb_ntree not found" fi if [ ! -x bin/arb_ntree ]; then err "bin/arb_ntree not executable" fi else err "Error in uncompressing or untaring $1" fi } separator echo ' Note: - You may abort this script with ctrl-"C"' echo ' - You can rerun this script as often as you like' echo ' - Old ARB data will be kept if requested (in this case' echo ' you can simply change some options)' echo ' - Pressing will select the value in brackets' separator echo 'Please answer some questions:' separator echo 'Where would you like to install ARB?' echo ' ARB is not a single program but a set of programs, datafiles ...' echo ' To install ARB, all files will be stored in a single directory.' echo '' echo ' This script will create that directory, copy all needed files and' echo ' sets permissions correctly.' echo '' echo ' Please note that you will need write permission at the destination.' echo '' if [ "$EUID" -ne 0 ]; then # normal user ARBHOMED=${HOME}/arb echo ' - to install ARB inside your home directory, enter "'${ARBHOMED}'"' echo ' - otherwise press Ctrl-C now to abort installation and' echo ' rerun this script using:' echo ' sudo bash arb_install.sh' else # root user ARBHOMED=/usr/arb echo ' - to install ARB for all users, enter "'${ARBHOMED}'"' fi echo '' if [ "$ARBHOME" != "" ]; then if test -f $ARBHOME/lib/arb_tcp.dat; then echo " Note: There seems to be an existing arb installation at" echo " ${ARBHOME}" echo '' fi fi echo "Enter full installation path: [${ARBHOME:-${ARBHOMED}}]" read ARBHOMEI echo echo if [ "$ARBHOMEI" = "" ]; then ARBHOME="${ARBHOME:-${ARBHOMED}}"; else ARBHOME="${ARBHOMEI}"; fi # check for some really unwanted characters in path: AH_NS=$(elim_invalid_chars ${ARBHOME}) if [ ! "$AH_NS" = "$ARBHOME" ]; then separator if [ ! "$AH_NS" = "" ]; then echo "Note: the path '$AH_NS' would be ok.." fi err "The specified path '$ARBHOME' contains invalid characters." fi cwd=`pwd` if [ ! -f arb.tgz ]; then if [ -e arb-*.tgz ]; then # link any arb-*.tgz to arb.tgz ln -s arb-*.tgz arb.tgz ls -al arb.tgz arb-*.tgz if [ ! -L arb.tgz ]; then err "Failed to link any arb-tarball to arb.tgz (maybe there are multiple arb-*.tgz in this directory)" fi else err "Expected exactly one arb-*.tgz in current directory." fi else ls -al arb.tgz arb-*.tgz fi if [ ! -f arb.tgz ]; then if [ -L arb.tgz ]; then rm arb.tgz err "arb.tgz does not link to a file - removed link" else err "arb.tgz is neither file nor link - can't handle" fi fi 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 separator echo 'The destination directory' echo " $ARBHOME" echo 'already exists!' if [ -z "$(ls -A ${ARBHOME})" ]; then echo "Note: directory is empty and will be used for arb installation." else echo ' You may now' echo ' * either delete the old arb directory completely' echo ' * or only update/change options of the old version.' echo 'Delete old directory (y/n)[n]?' read delete_dir echo case "$delete_dir" in y) if rm -r $ARBHOME/* ;then echo ">>> all data in $ARBHOME deleted" else cont "failed to delete files 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 fi 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 $ARBHOME ARBHOME=`pwd` if test -d lib/pictures; then separator echo "Old ARB package found (type n to change only some options)." echo " Do you want to update the old package: (y/n)[y]" read var; case "$var" in n) echo "Old version unchanged";; *) echo "updating ARB"; untar arb.tgz;; esac else untar arb.tgz; fi separator 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 $pt_dir pts;) esac separator echo 'Who is responsible for the PT_SERVER index files ?' echo ' Answer y: if you trust your users (less administration; recommended)' echo ' n: if PT_SERVER files shall only be changable by administrator' echo ' or simply press return to keep the settings of an old installation.' echo 'Should everybody be allowed to build/update PT_SERVER files (y/n/dont_change)[dont_change]?' read var echo case "$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 separator echo 'NameServer installation' echo ' The NameServer is a program, 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 ${ARBHOME}/lib/nas/names.dat" chmod 755 lib/nas chmod 644 lib/nas/*;; *) echo ">>> flags unchanged";; esac separator echo 'Networking' echo ' To speed up calculation one special host can be assigned as' echo ' the PT_SERVER host. That means that all database search is done' echo ' on that host. This saves computer resources as different users' echo ' may share one server.' echo ' To get the best results this host "H" should:' echo ' 1. be fast,' echo ' 2. have a lot of real memory (>=64 meg),' echo ' 3. have a lot of swap space (>=400 meg),' echo ' 4. allow all users to run "ssh H ...",' echo ' 5. contain the discs with the PT_SERVER files.' echo ' n You want to assign a special Network host' echo ' s You have a Stand alone computer' if test "X$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) separator 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 separator echo ">>> Installation Complete" separator 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 new terminal window 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 if [ "$EUID" -eq 0 ]; then # only shown to root user: echo "" echo "Note for sysadmins:" echo " In order to provide arb for all users, edit one or several" echo " of the global shell init files in /etc (e.g. /etc/bash.bashrc)" echo " in the same manner as described above for the" echo " local shell init files." echo "" echo " Note for unintended sysadmins:" echo " To edit the global bash init file use e.g." echo " sudo nano /etc/bash.bashrc" echo " Insert the 'arb' alias on a separate line." fi echo "" echo "Please read the files" echo " $ARBHOME/arb_INSTALL.txt" echo " $ARBHOME/arb_UBUNTU.txt (if you're using ubuntu)" echo "about additional libraries and tools needed by ARB." echo "" echo "After you have installed everything and performed the changes to your init file," echo "open a new terminal window and start arb by typing" echo "" echo " arb" echo "" echo "Have much fun using ARB" echo "ARB Team " echo ""