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<global>
         ...
        <models>
            <timer>
                <class>Apptha_Timer_Model</class>
                <resourceModel>apptha_timer_model_resource</resourceModel>
            </timer>
            <apptha_timer_model_resource>
                <class>Apptha_Timer_Model_Resource</class>
            </apptha_timer_model_resource>
        </models>
        <resources>
            <timer_setup>
                <setup>
                    <module>Apptha_Timer</module>
                    <class>Apptha_Timer_Model_Resource_Eav_Mysql4_Setup</class>
                </setup>

                <connection>
                    <use>core_setup</use>
                </connection>
            </timer_setup>
            <timer_write>
                <connection>
                    <use>core_write</use>
                </connection>
            </timer_write>
            <timer_read>
                <connection>
                    <use>core_read</use>
                </connection>
            </timer_read>
        </resources>
    </global>

The error says: Warning: include(Apptha/Timer/Model/Resource/Eav/Mysql4/Setup.php): failed to open stream: No such file or directory in /var/www/html/lib/Varien/Autoload.php on line 94 but the file does exist in the right folder and class name.

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This line in the config <class>Apptha_Timer_Model_Resource_Eav_Mysql4_Setup</class> says that for the db schema install/upgrade, magento will use your class Apptha_Timer_Model_Resource_Eav_Mysql4_Setup to execute the install./upgrade scripts.
If you don't plan do do anything fancy during the install/upgrade for table schemas you can just remove that line from the config.
If you have custom logic in the install/upgrade scripts you need to create the class and it should extend Mage_Core_Model_Resource_Setup or any other class that extends Mage_Core_Model_Resource_Setup.
For example, if you need to add some eav attributes or attribute sets you can extend Mage_Eav_Model_Entity_Setup, or if you need to modify something related to orders you can extend Mage_Sales_Model_Entity_Setup or Mage_Sales_Model_Resource_Setup.

If you say the file exists, make sure there is no typo in the class or folder name.

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