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, 08:37, 31 October 2014
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| | == Running the Demo on Already Running Node == | | == Running the Demo on Already Running Node == |
| − | === Examine the Setup ===
| + | {{GotCloud: Amazon Demo Setup}} |
| − | #After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: <code>/home/ubuntu</code>
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| − | ## You can check this by doing:
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| − | ##:<pre>pwd</pre>
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| − | ##* This should output: <code>/home/ubuntu</code>
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| − | ## Take a look at the contents of the ubuntu user home directory
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| − | ##: <pre>ls</pre>
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| − | ##* This should output be 2 directories, <code>example</code> and <code>gotcloud</code>
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| − | ##** The <code>example</code> directory contains the files for this demo
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| − | ##** The <code>gotcloud</code> directory contains the gotcloud programs and pre-compiled source
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| − | #:[[File:DemoHome.png|400px]]
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| − | # Look at the example input files:
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| − | #:<pre>ls example</pre>
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| − | #:[[File:ExampleFiles.png|400px]]
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| − | #:# <code>bam.list</code> contains the list of BAM files per sample
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| − | #:# <code>bams</code> is a subdirectory containing the BAM files for this demo
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| − | #:# <code>test.bed</code> contains the region we want to process in this demo
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| − | #:#* 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
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| − | #:#:[[File:BedContents.png|400px]]
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| − | #:# <code>test.conf</code> contains the settings we want GotCloud to use for this run
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| − | #:#:[[File:ConfContents.png|400px]]
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| − | #:#:* For the demo, we want to tell GotCloud:
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| − | #:#:*# The list of bams to use: <code>BAM_LIST = example/bam.list</code>
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| − | #:#:*# The region to process rather than the whole genome: <code>UNIFORM_TARGET_BED = example/test.bed</code>
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| − | #:#:*# The chromosomes to process. The default chromosomes are 1-22 & X, but we only want to process chromosome 22: <code>CHRS = 22</code>
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| | === Run GotCloud SnpCall === | | === Run GotCloud SnpCall === |
