Issue with configuring Atomikos on a Spring Boot /

I am trying to get Atomikos to work with my Spring Boot/Spring Batch application.

Here is are the relevant portions of my code:

Datasource config:

@Configuration
public class DatasourceConfiguration extends AbstractCloudConfig {

    @Bean
    @Qualifier("batch_database")
    public DataSource batchDatasource() {
        return connectionFactory().dataSource("batch_database");
    }

    @Bean
    public PlatformTransactionManager transactionManager(){
        return  new JtaTransactionManager();
    }

    @Bean
    public TaskConfigurer configurer(){
        return new DefaultTaskConfigurer(batchDatasource());
    }
}

Atomikos auto-config dependency:

compile("org.springframework.boot:spring-boot-starter-jta-atomikos")

My application.properties:

spring.datasource.application.driver-class-name=org.postgresql.xa.PGXADataSource
spring.datasource.batch.driver-class-name=org.postgresql.xa.PGXADataSource

Here is the auto-configuration report:

   DataSourceTransactionManagerAutoConfiguration matched
      - @ConditionalOnClass classes found: org.springframework.jdbc.core.JdbcTemplate,org.springframework.transaction.PlatformTransactionManager (OnClassCondition)

   DataSourceTransactionManagerAutoConfiguration.DataSourceTransactionManagerConfiguration matched
      - @ConditionalOnBean (types: javax.sql.DataSource; SearchStrategy: all) found the following [batchDatasource, applicationDatasource, batch_database, application_database, database] (OnBeanCondition)

   AtomikosJtaConfiguration did not match
      - @ConditionalOnClass classes found: org.springframework.transaction.jta.JtaTransactionManager,com.atomikos.icatch.jta.UserTransactionManager (OnClassCondition)
      - @ConditionalOnMissingBean (types: org.springframework.transaction.PlatformTransactionManager; SearchStrategy: all) found the following [transactionManager] (OnBeanCondition)

   AtomikosJtaConfiguration.AtomikosJtaJmsConfiguration did not match
      - required @ConditionalOnClass classes not found: javax.jms.Message (OnClassCondition)
      - Ancestor 'org.springframework.boot.autoconfigure.transaction.jta.AtomikosJtaConfiguration' did not match (ConditionEvaluationReport.AncestorsMatchedCondition)

I am not sure why Atomikos is not auto-configured... Can anyone please help?

edit: I have commented out the JTA transactionManager bean and I now get the following auto-configuration report:

   DataSourceTransactionManagerAutoConfiguration matched
      - @ConditionalOnClass classes found: org.springframework.jdbc.core.JdbcTemplate,org.springframework.transaction.PlatformTransactionManager (OnClassCondition)

    DataSourceTransactionManagerAutoConfiguration.DataSourceTransactionManagerConfiguration matched
          - @ConditionalOnBean (types: javax.sql.DataSource; SearchStrategy: all) found the following [batchDatasource, applicationDatasource, batch_database, application_database, database] (OnBeanCondition)

   TransactionAutoConfiguration matched
      - @ConditionalOnClass classes found: org.springframework.transaction.support.TransactionTemplate,org.springframework.transaction.PlatformTransactionManager (OnClassCondition)
      - @ConditionalOnSingleCandidate (types: org.springframework.transaction.PlatformTransactionManager; SearchStrategy: all) found a primary candidate amongst the following [transactionManager] (OnBeanCondition)

   AtomikosJtaConfiguration did not match
      - @ConditionalOnClass classes found: org.springframework.transaction.jta.JtaTransactionManager,com.atomikos.icatch.jta.UserTransactionManager (OnClassCondition)
      - @ConditionalOnMissingBean (types: org.springframework.transaction.PlatformTransactionManager; SearchStrategy: all) found the following [transactionManager] (OnBeanCondition)

   AtomikosJtaConfiguration.AtomikosJtaJmsConfiguration did not match
      - required @ConditionalOnClass classes not found: javax.jms.Message (OnClassCondition)
      - Ancestor 'org.springframework.boot.autoconfigure.transaction.jta.AtomikosJtaConfiguration' did not match (ConditionEvaluationReport.AncestorsMatchedCondition)

How can I make sure the Atomikos transaction manager is picked up?

edit 2: I have excluded TransactionManager classes as follows:

@EnableAutoConfiguration(exclude = {DataSourceTransactionManagerAutoConfiguration.class, TransactionAutoConfiguration.class})

but I seems that SimpleBatchConfiguration and SimpleTaskConfiguration still force one of several TransactionManager class(es) on me:

2016-07-12 11:27:57.846  INFO 4851 --- [           main] o.s.b.f.s.DefaultListableBeanFactory     : Overriding bean definition for bean 'transactionManager' with a different definition: replacing [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.springframework.batch.core.configuration.annotation.SimpleBatchConfiguration; factoryMethodName=transactionManager; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/springframework/batch/core/configuration/annotation/SimpleBatchConfiguration.class]] with [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.springframework.cloud.task.configuration.SimpleTaskConfiguration; factoryMethodName=transactionManager; initMethodName=null; destroyMethodName=(inferred); defined in org.springframework.cloud.task.configuration.SimpleTaskConfiguration]

causing the AtomikosJtaConfiguration not to match...

Can someone please advise a best practice in order to get Atomikos auto-configuration to work?

You don't need to add Atomikos or Bitronix to specify a PlatformTransactionManager for your datasource. See Entities not persisting. Are RepositoryItemWriter & SimpleJpaWriter thread-safe?.