browserStartup.sh

#!/bin/bash
# file to start environment necessary for the genome browser, currently only used on OSX:
# starts mysql and apache
# with parameter "-e" modifies PATH and restarts a login shell
set -e

APACHEDIR=/usr/local/apache
BASEDIR=$APACHEDIR/ext

MYSQLPID=$BASEDIR/logs/mysql.pid

# try to kill and start mysql
if [ -f $BASEDIR/logs/mysql.pid ]; then
   kill `cat $BASEDIR/logs/mysql.pid` 2> /dev/null || true
   sleep 3
fi
if [ -f $BASEDIR/bin/mysqld_safe ]; then
    $BASEDIR/bin/mysqld_safe --defaults-file=$BASEDIR/my.cnf --user=_mysql --pid-file=$MYSQLPID &
fi

sleep 5

# try to kill and start apache
if [ -f "$BASEDIR/logs/httpd.pid" ]; then
   kill `cat $BASEDIR/logs/httpd.pid` 2> /dev/null || true
fi
if [ -f $BASEDIR/bin/httpd ]; then
   $BASEDIR/bin/httpd -d "$BASEDIR"
fi

if [ ! -f $MYSQLPID ]; then
    echo File $MYSQLPID does not exist after mysql startup.
    echo Apparently Mysql is unable to start.
    echo The error log file location was output to the screen by myqld above.
    echo Some ideas on the reasons might be available in $BASEDIR/my.cnf or the mysql error log file
    exit 250
fi

if [[ "$1" == "-e" ]]; then
    export PATH="$BASEDIR/bin:$PATH"
    export MYSQLINC=$APACHEDIR/ext/include
    export MYSQLLIBS="/$APACHEDIR/ext/lib/libmysqlclient.a -lz -lc++"
    export SSLDIR=$APACHEDIR/ext/include
    export USE_SSL=1
    export PNGLIB=$APACHEDIR/ext/lib/libpng.a
    # careful - PNGINCL is the only option that requires the -I prefix
    export PNGINCL=-I$APACHEDIR/ext/include
    export CGI_BIN=$APACHEDIR/cgi-bin
    export SAMTABIXDIR=$APACHEDIR/kent/samtabix
    export USE_SAMTABIX=1
    export SCRIPTS=$APACHEDIR/util
    export BINDIR=$APACHEDIR/util

    # find parent process name of this process and spawn new shell if it's bash or tcsh
    parent=`ps -p $PPID -o comm=`
    
    if [[ "$parent" == "tcsh" ]]; then
       echo Adapting PATH and starting new tcsh
       tcsh
    elif [[ "$parent" == "bash" ]]; then
       echo Adapting PATH and starting new bash
       bash -l
    else
       echo Not changing PATH, parent is not bash or tcsh
    fi
fi