Setup Magento permissions/ownership following the recommendations of the official article : http://devdocs.magento.com/guides/m1x/install/installer-privileges_after.html

mage-set-perms

#!/bin/bash

#Check root access

if [ "$UID" != 0 ]
then
   echo "This shell script must be run as root."
   exit 2
fi

#Variables declaration

GROUP_ACCESS=
WEB_USER=
WEB_GROUP=
ROOT_DIR='.' #Web root directory
VAR_DIR="$ROOT_DIR/var/"
MEDIA_DIR="$ROOT_DIR/media/"
INCLUDES_DIR="$ROOT_DIR/includes"

if [ -n "$1" ] && [ -d "$1" ]
then
   ROOT_DIR="$1"
fi

#Functions declaration

check_magento_dir()
{
   if  [ ! -f "$1/app/Mage.php" ]
   then
      error 'Magento installation directory not found!'
   fi
}

error()
{
   echo "$@" 1>&2
   exit 1
}

warning()
{
   echo "$@" 1>&2
}

set_user_perms()
{
   find "$ROOT_DIR" \( -path "$VAR_DIR" -o -path "$MEDIA_DIR" -o -path "$INCLUDE_DIR" \) -type d \! -perm 500 -exec chmod 500 {} \;
   find "$ROOT_DIR" -type f \! -perm 400 -exec chmod 400 {} \;
   find "$VAR_DIR" -type d \! -perm 700 -exec chmod 700 {} \;
   find "$VAR_DIR" -type f \! -perm 600 -exec chmod 600 {} \;
   find "$MEDIA_DIR" -type d \! -perm 700 -exec chmod 700 {} \;
   find "$MEDIA_DIR" -type f \! -perm 600 -exec chmod 600 {} \;

   if [ -e "$INCLUDES_DIR" ] && [ $(stat -c "%a" "$INCLUDES_DIR") != 700 ]
   then
        chmod 700 "$INCLUDES_DIR"
   fi

   if [ -e "$INCLUDES_DIR/config.php" ] && [ $(stat -c "%a" "$INCLUDES_DIR/config.php") != 600 ]
   then
        chmod 600 "$INCLUDES_DIR/config.php"
   fi

}

set_user_and_group_perms()
{
   find "$ROOT_DIR" \( -path "$VAR_DIR" -o -path "$MEDIA_DIR" -o -path "$INCLUDE_DIR" \) -type d \! -perm 550 -exec chmod 550 {} \;
   find "$ROOT_DIR" -type f \! -perm 440 -exec chmod 440 {} \;
   find "$VAR_DIR" -type d \! -perm 770 -exec chmod 770 {} \;
   find "$VAR_DIR" -type f \! -perm 660 -exec chmod 660 {} \;
   find "$MEDIA_DIR" -type d \! -perm 770 -exec chmod 770 {} \;
   find "$MEDIA_DIR" -type f \! -perm 660 -exec chmod 660 {} \;

   if [ -e "$INCLUDES_DIR" ] && [ $(stat -c "%a" "$INCLUDES_DIR") != 770 ]
   then
        chmod 770 "$INCLUDES_DIR"
   fi

   if [ -e "$INCLUDES_DIR/config.php" ] && [ $(stat -c "%a" "$INCLUDES_DIR/config.php") != 660 ]
   then
        chmod 660 "$INCLUDES_DIR/config.php"
    fi

}

chown_magento_dir()
{
   #if [ $(stat -c "%U" "$ROOT_DIR") != "$WEB_USER" ] && [ $(stat -c "%G" "$ROOT_DIR") != "$WEB_GROUP" ]
   #then
        chown -R "$WEB_USER:$WEB_GROUP" "$ROOT_DIR"
   #fi
}

#Main

check_magento_dir "$ROOT_DIR"

while true
do
   read -p "Enter a valid Web User account: " user

   if id -u "$user" > /dev/null 2>&1
   then
      WEB_USER=$user
      break;
   else
      warning "No such user: $user"
   fi
done

while true
do
   read -p "Enter a valid Web Group account: " group

   if getent group "$group" > /dev/null 2>&1
   then
      WEB_GROUP=$group
      break;
   else
       warning "No such group: $group"
   fi
done

read -r -p "Allow group access ? [y/N] " answer

if [[ $answer =~ ^([yY][eE][sS]|[yY])$ ]]
then
    GROUP_ACCESS=true
fi

echo -n "Changing ownership of : $ROOT_DIR ..."

chown_magento_dir

echo "Done!"

echo -n "Setting permissions for : $ROOT_DIR ..."

if [ -z $GROUP_ACCESS ]
then
   set_user_perms
else
   set_user_and_group_perms
fi

echo "Done!"