Here is the configuration of mybatis and jpa in spring framework. Mybatis and jpa are different framework so you cannot use mybatis as a JPA framework. Feel free to ask any question if you cannot catch up the configuration.
package com.mastering.springbatch.config;
import org.apache.ibatis.session.SqlSessionFactory;
import org.mybatis.spring.SqlSessionFactoryBean;
import org.springframework.boot.autoconfigure.domain.EntityScan;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.jdbc.datasource.DriverManagerDataSource;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.JpaVendorAdapter;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.sql.DataSource;
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(
        basePackages = {"com.mastering.springbatch.dao",
                "com.mastering.springbatch.repository"})
@EntityScan("com.mastering.springbatch.entity")
public class DataConfig {
    private final String ENTITY_PACKAGE = "com.mastering.springbatch.entity";
    private DriverManagerDataSource dataSource;
    @Primary
    @Bean(value = "customDataSource")
    @ConfigurationProperties(prefix = "spring.datasource")
    public DataSource dataSource() {
        DriverManagerDataSource dataSource = new DriverManagerDataSource();
        this.dataSource = dataSource;
        return dataSource;
    }
    @Primary
    @Bean(value = "entityManagerFactory")
    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
        LocalContainerEntityManagerFactoryBean emf =
                new LocalContainerEntityManagerFactoryBean();
        emf.setPackagesToScan(ENTITY_PACKAGE);
        emf.setDataSource(dataSource());
        emf.setJpaVendorAdapter(jpaVendorAdapter());
        return emf;
    }
    @Primary
    @Bean(value = "sqlSessionFactory")
    public SqlSessionFactory sqlSessionFactory() throws Exception {
        SqlSessionFactoryBean factoryBean = new SqlSessionFactoryBean();
        factoryBean.setDataSource(dataSource());
        return factoryBean.getObject();
    }
    @Primary
    @Bean(name = "transactionManager")
    public PlatformTransactionManager transactionManager() {
        JpaTransactionManager tm = new JpaTransactionManager();
        tm.setEntityManagerFactory(entityManagerFactory().getObject());
        return tm;
    }
    private JpaVendorAdapter jpaVendorAdapter() {
        HibernateJpaVendorAdapter jpaVendorAdapter = new HibernateJpaVendorAdapter();
        jpaVendorAdapter.setShowSql(true);
        jpaVendorAdapter.setGenerateDdl(true);
        jpaVendorAdapter.setDatabasePlatform("org.hibernate.dialect.MySQLDialect");
        return jpaVendorAdapter;
    }
}
here is the build.gradle file
buildscript {
    ext {
        springBootVersion = '2.1.8.RELEASE'
        springBootDepManagementVersion = '1.0.8.RELEASE'
    }
    repositories {
        mavenLocal()
        mavenCentral()
    }
    dependencies {
        classpath("org.springframework.boot:spring-boot-gradle-plugin:${springBootVersion}")
        classpath "io.spring.gradle:dependency-management-plugin:${springBootDepManagementVersion}"
    }
}
apply plugin: 'org.springframework.boot'
apply plugin: 'io.spring.dependency-management'
apply plugin: 'java'
apply plugin: 'idea'
group 'com.learning'
version '1.0-SNAPSHOT'
sourceCompatibility = 1.8
configurations {
    implementation.exclude module: "spring-boot-starter-tomcat"
}
repositories {
    mavenLocal()
    mavenCentral()
}
dependencies {
    compile 'org.mybatis:mybatis:3.5.0'
    compile 'org.mybatis:mybatis-spring:2.0.0'
    implementation("org.springframework.boot:spring-boot-starter-data-jpa")
    implementation("org.springframework.boot:spring-boot-starter-batch")
    implementation("org.springframework.boot:spring-boot-starter-web")
    
    implementation("mysql:mysql-connector-java:8.0.14")
    
//    implementation("io.springfox:springfox-swagger2:2.7.0")
//    implementation("io.springfox:springfox-swagger-ui:2.7.0")
    
    implementation("org.projectlombok:lombok:1.18.10")
    annotationProcessor("org.projectlombok:lombok:1.18.10")
    compile group: 'commons-io', name: 'commons-io', version: '2.6'
    testAnnotationProcessor("org.projectlombok:lombok:1.18.10")
    testCompile("junit:junit:4.12")
    testCompile("org.mockito:mockito-core:2.1.0")
    testCompile("org.springframework.boot:spring-boot-starter-test")
}
springBoot {
    buildInfo()
}