#!/bin/bash bold=$(tput bold) underline=$(tput smul) normal=$(tput sgr0) echoerr() { cat <<< "$@" 1>&2 } # error message function (nested exit): trap "exit 1" TERM export ARBINST_SCRIPT_PID=$$ err() { echoerr "Error in `basename $0`:" echoerr "${bold} $@${normal}" echoerr "Please fix and then rerun script!" kill -s TERM $ARBINST_SCRIPT_PID } separator() { echo '' } separator echo "${bold}${underline}Welcome to the ARB Package${normal}" 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: $@" 1>&2 echo "${bold}Do you want to continue [y]${normal}" read var case "$var" in n) err "Script aborted by user" ;; *) echo 'Continuing...' ;; esac } untar() { local TGZ="$1"; shift # remove old DEPOT BUG rm -f DEPOT/gde/bin if [ ! -r "${TGZ}" ]; then err "Cannot find or read file '${TGZ}'" fi if gunzip --stdout "${TGZ}" | tar xfv -; then echo ">>> ${TGZ} uncompressed and untared" if [ ! -e bin/arb_ntree ]; then err "bin/arb_ntree not found (wrong archive?)" fi if [ ! -x bin/arb_ntree ]; then err "bin/arb_ntree not executable (wrong archive?)" fi else err "Failed to uncompress/untar '${TGZ}'" fi } arb_realpath() { # replacement for 'realpath' # # Note: this function is duplicated in SH/arb_path.sh@arb_realpath local FILE="$1"; shift local REALPATH=$(realpath "$FILE" 2>/dev/null ) local READLINK=$(readlink -f "$FILE" 2>/dev/null ) if [ -z "${REALPATH}" ]; then if [ -z "${READLINK}" ]; then echoerr "Warning: neighter realpath nor readlink works here" if [ -e "${FILE}" ]; then local PWDFILE="$(pwd)/${FILE}" if [ -e "${PWDFILE}" ]; then echo "${PWDFILE}" else echo "${FILE}" fi else echo "${FILE}" fi else echo "${READLINK}" fi else if [ -z "${READLINK}" ]; then echo "${REALPATH}" else if [ "${READLINK}" != "${REALPATH}" ]; then echoerr "Warning: realpath and readlink differ (REALPATH=${REALPATH} READLINK=${READLINK})" fi echo "${REALPATH}" fi fi } # -------------------------------------------------- # detect input archives: separator ARB_TGZ= SINA_TGZ= for TGZ in arb*.tgz; do NOSINA=${TGZ%-sina-fat.tgz} if [ "${NOSINA}" = "$TGZ" ]; then if [ -z "${ARB_TGZ}" ]; then ARB_TGZ="${TGZ}" else echo "Found two arb archives:" ls -al -h "${ARB_TGZ}" "${TGZ}" echo "" err "cannot decide which to use. Please remove one of these!" fi else if [ -z "${SINA_TGZ}" ]; then SINA_TGZ="${TGZ}" else echo "Found two sina archives:" ls -al -h "${SINA_TGZ}" "${TGZ}" echo "" err "cannot decide which to use. Please remove one of these!" fi fi done if [ -n "${SINA_TGZ}" ]; then SINA_TGZ=$(arb_realpath "${SINA_TGZ}") echo "Detected sina tarball: ${SINA_TGZ}" fi if [ -z "${ARB_TGZ}" ]; then echo "For available arb versions please refer to" echo " http://bugs.arb-home.de/wiki#ARBversions" separator err "No arb tarball found in `pwd`" fi ARB_TGZ=$(arb_realpath "${ARB_TGZ}") echo "Detected arb tarball: ${ARB_TGZ}" # -------------------------------------------------- # general instructions + ask for destination: separator echo ' Note: - You may abort this script with ctrl-"C"' echo ' - You can rerun this script as often as you like' echo ' - Old ARB data will be kept if requested (in this case' echo ' you can simply change some options)' echo ' - Pressing will select the value in brackets' separator echo "${underline}Please answer some questions:${normal}" separator echo 'Where would you like to install ARB?' echo ' ARB is not a single program but a set of programs, datafiles ...' echo ' To install ARB, all files will be stored in a single directory.' separator echo ' This script will create that directory, copy all needed files and' echo ' sets permissions correctly.' separator echo ' Please note that you will need write permission at the destination.' separator if [ "$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 "'${ARBHOMED}'"' fi separator if [ "$ARBHOME" != "" ]; then if test -f $ARBHOME/lib/arb_tcp.dat; then echo " Note: There seems to be an existing arb installation at" echo " ${ARBHOME}" separator fi fi echo "${bold}Enter full installation path: [${ARBHOME:-${ARBHOMED}}]${normal}" read ARBHOMEI separator if [ "$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 ARBHOME=$(arb_realpath "${ARBHOME}") # -------------------------------------------------- # handle existing arb installation: if test -d $ARBHOME; then 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 ARB_TCP_BAK=arb_tcp_`date +%Y%m%d`.dat if [ ! -e ${ARB_TCP_BAK} -a -e $ARBHOME/lib/arb_tcp.dat ]; then echo '[creating backup copy of arb_tcp.dat in download directory]' cp $ARBHOME/lib/arb_tcp.dat ${ARB_TCP_BAK} fi echo ' You may now' echo ' * either delete the old arb directory completely' echo ' * or only update/change options of the old version.' echo "${bold}Delete old directory? (y/n)[n]${normal}" read delete_dir echo case "$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 $ARBHOME ARBHOME=`pwd` if [ -d lib/pictures ]; then separator echo "${underline}Old ARB package found${normal} (type n to change only some options)." echo "${bold} Do you want to update the old package? (y/n)[y]${normal}" read var; case "$var" in n) echo "Old version unchanged" ;; *) echo "updating ARB"; untar "${ARB_TGZ}" ;; esac else untar "${ARB_TGZ}" fi # -------------------------------------------------- # configure ptserver: separator echo "${underline}Specify PT_SERVER files location${normal}" 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 "${bold}Enter path:${normal}" 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 ${ARBHOME}/lib/pts; then echo ">>> data in default location found" echo "${bold}Do you want to remove old ptserver data (recommended)? [y]${normal}" read ANSWER case "$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 $pt_dir pts;) esac separator echo 'Who is responsible for the PT_SERVER index files?' echo ' Answer y: if you trust your users (less administration; recommended)' echo ' n: if PT_SERVER files shall only be changable by administrator' echo ' or simply press return to keep the settings of an old installation.' echo "${bold}Should everybody be allowed to build/update PT_SERVER files? (y/n/dont_change)[dont_change]${normal}" read var echo case "$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 ">>> permissions of lib/pts remain unchanged";; esac # -------------------------------------------------- # configure nameserver: separator echo "${underline}NameServer installation${normal}" 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 $ARBHOME/lib/nas/names.dat' echo ' Answer y: if all users may import foreign databases' echo ' n: if there are some mean untrusty users' echo ' or simply press return to keep the old settings' echo "${bold}Do you trust your users? (y/n/dont_change)[dont_change]${normal}" read var echo case "$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 ${ARBHOME}/lib/nas/names.dat" chmod 755 lib/nas chmod 644 lib/nas/*;; *) echo ">>> permissions of lib/nas remain unchanged";; esac # -------------------------------------------------- # setup arb_tcp.dat: separator echo "${underline}Networking${normal}" echo ' To speed up calculation one special host can be assigned as' echo ' the PT_SERVER host. That means that all database search is done' echo ' on that host. This saves computer resources as different users' echo ' may share one server.' echo ' To get the best results this host "H" should:' echo ' 1. be fast,' echo ' 2. have a lot of real memory (>=64 meg),' echo ' 3. have a lot of swap space (>=400 meg),' echo ' 4. allow all users to run "ssh H ...",' echo ' 5. contain the discs with the PT_SERVER files.' echo ' n You want to assign a special Network host' echo ' s You have a Stand alone computer' if test "X$bckup" != "X"; then echo ' o Use information of already installed ARB' echo "${bold}Choose (s/n/o)[s]${normal}" else echo "${bold}Choose (s/n)[s]${normal}" 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 # -------------------------------------------------- # install sina: separator echo "${underline}SINA integration${normal}" if [ -n "${SINA_TGZ}" ]; then echo "Detected sina archive: ${SINA_TGZ}" if [ -x bin/sina ]; then echo "Note: The installed arb already seems to contain sina." echo " => will not install another sina!" else INSTALL_SINA=0 HAVE_SINA=0 # check for installation via SH/arb_sina_install_from_fat_tarball.sh if [ -d bin/fatsina ]; then echo "Note: there is already another sina installed from a tarball." HAVE_SINA=1 echo "${bold} Do you want to update the sina installation? (y/n)[y]${normal}" else echo "${bold} Do you want to install sina into arb? (y/n)[y]${normal}" INSTALL_SINA=1 fi read var; case "$var" in n) if [ ${HAVE_SINA} = 1 ]; then echo "Old sina version unchanged." else echo "Will not install sina." fi ;; *) if [ ${HAVE_SINA} = 1 ]; then echo "updating SINA from ${SINA_TGZ}"; SH/arb_sina_install_from_fat_tarball.sh UNINSTALL "${ARBHOME}" else echo "installing SINA from ${SINA_TGZ}"; fi SH/arb_sina_install_from_fat_tarball.sh "${SINA_TGZ}" "${ARBHOME}" ;; esac fi else if [ ! -x bin/sina ]; then if [ ! -d bin/fatsina ]; then echo "No sina installed with arb." echo "Hint: the installation script will attempt to install sina for you," echo " if you download an arb-XXX-fat-sina.tgz and" echo " save it into ${DL_DIR}" fi fi fi # -------------------------------------------------- # finish + print instructions for setup separator echo "${bold}>>> ARB installation completed${normal}" separator SHELL_ANS=0 echo "${underline}Finally, you have to tell your system where to find arb${normal}" echo "First find out which shell you are using, by opening a new terminal window and typing" echo ' echo $SHELL' echo "" echo "Depending on what is your shell there are several choices:" echo "" echo " 1. Change your local .profile or .bashrc (if you are using ksh/bash, which" echo " is the default shell for Linux)" echo " 2. Change your local .cshrc file (if you are using csh/tcsh)" echo " 3. Create an alias for arb (any shell)" echo " 4. I don't want to edit anything (any shell)" echo "" echo "${bold}Enter (1,2,3 or 4) to achieve further installation instructions:${normal}" while [ "$SHELL_ANS" = "0" ]; do read var separator case "$var" in 1) echo '******************************************************'; echo "${bold}add the following lines to your ~/.profile${normal}"; echo "${bold}or to your ~/.bashrc for bash-users${normal}"; echo '******************************************************'; echo " ARBHOME=$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'; separator echo 'enter the following command:'; echo ' . ~/.profile' SHELL_ANS=1 ;; 2) echo '******************************************'; echo "${bold}add the following lines to your ~/.cshrc${normal}"; 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'; separator echo 'enter the following command:'; echo ' source ~/.cshrc' SHELL_ANS=1 ;; 3) echo '**************************************************'; echo "${bold}add one of the following lines to your init file${normal}"; 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 ;; 4) echo "Note: You will need to specify the full path to start arb."; SHELL_ANS=2 ;; *) echo 'wrong answer' ;; esac done if [ "$EUID" -eq 0 ]; then # only shown to root user: separator echo "${underline}Note for sysadmins:${normal}" 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." separator 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 separator 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." separator 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" separator if [ $SHELL_ANS = 2 ]; then echo " $ARBHOME/bin/arb"; else echo " arb" fi separator echo "${bold}Have much fun using ARB${normal}" echo "ARB Team " separator