root/tags/release_2007_12/arb_install.sh

#!/bin/sh

# 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 <return> 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 (40 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 "PATH ? [${ARBHOME:-/usr/arb}]"
read ARBHOMEI
echo
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 $ARBHOME; then
                seperator
                echo 'The destination directory already exists'
                echo '  You can delete the old directory before installing ARB'
                echo '  or only update/change options of the old version.'
                echo 'Delete old directory (y/n)[n]?'
                read delete_dir
                echo
                case "$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 '          <ARB_NTREE/Probes/PT_SERVER admin/Build server>'
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. <CR> - (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
( $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,"
    echo "       which is the default shell for Linux)"
    echo "    2. Change your local .cshrc file (if you are using csh/tcsh)"
    echo "    3. Create an alias:   alias arb=$ARBHOME/bin/arb"
    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 "     alias arb=$ARBHOME/bin/arb";
             echo "     alias arb '$ARBHOME/bin/arb'";
             echo "and reread the file or"
             echo "type one of these lines at the command prompt."
             SHELL_ANS=1 ;;
          *)
             echo 'Wrong answer';;
        esac
    done

        echo ""
        echo "Note for sysadmins: You might want to edit the global init files"
        echo "                    in /etc to provide arb for all users."
        echo ""
        echo "When you performed these changes, you can start arb "
        echo "from a new shell by typing 'arb'"
        echo ""
        echo "Have much fun using ARB"
        echo "ARB Team <arb@arb-home.de>"
        echo ""

        unset host
        unset cwd
        unset ARBHOME
        unset delete_dir
        unset keep_debug
        unset pt_dir
        unset var