Changes

==Running the Automatic Test==

==Running the Automatic Test==

This verifies that GotCloud's alignment pipeline was installed correctly.

This will verify whether GotCloud was installed correctly.

To run the test case for the alignment pipeline automatically, change your current directory to GotCloud's root directory, and type in the following command:

*To run the test case for the alignment pipeline automatically, change your current directory to GotCloud's root directory, and type in the following command:

  bin/gen_biopipeline.pl --test OUTPUT_DIR

  bin/gen_biopipeline.pl --test OUTPUT_DIR

where OUTPUT_DIR is the directory where you want to store the test results.

where OUTPUT_DIR is the directory where you want to store the test results.

If you see "Test Passed", then you are ready to run a sample.

If you see "Test Passed", then you are ready to align samples.

 

 

*To run the test case for the variant-calling pipeline (UMAKE), change your current directory to GotCloud's root directory, and type in the following command:

 

 

 

If you see "Test Passed", then you are ready to call variants.