Template:GotCloud: Amazon Demo Setup

Examine the Setup

1. After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: /home/ubuntu
   1. You can check this by doing:

      pwd

      • This should output: /home/ubuntu
   2. Take a look at the contents of the ubuntu user home directory

      ls

      • This should output be 2 directories, example and gotcloud
        • The example directory contains the files for this demo
        • The gotcloud directory contains the gotcloud programs and pre-compiled source

   

2. Look at the example input files:

   ls example

   

   1. bam.list contains the list of BAM files per sample
   2. bams is a subdirectory containing the BAM files for this demo
   3. test.bed contains the region we want to process in this demo
      • To make the demo run faster, we only want to process a small region of chromosome 22. This file tells GotCloud the region. The region we are using is the APOL1 region

      

   4. test.conf contains the settings we want GotCloud to use for this run

      

      • For the demo, we want to tell GotCloud:
        1. The list of bams to use: BAM_LIST = example/bam.list
        2. The region to process rather than the whole genome: UNIFORM_TARGET_BED = example/test.bed
        3. The chromosomes to process. The default chromosomes are 1-22 & X, but we only want to process chromosome 22: CHRS = 22