Mktrost: Mktrost moved page GotCloud: Amazon Demo Setup to Template:GotCloud: Amazon Demo Setup

2014-10-31T12:38:06Z

Mktrost moved page GotCloud: Amazon Demo Setup to Template:GotCloud: Amazon Demo Setup

← Older revision	Revision as of 08:38, 31 October 2014
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Mktrost: Created page with "{{{hdr|===}}} Examine the Setup {{{hdr|===}}} #After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: `/home/ubuntu..."`


2014-10-31T12:37:17Z
Created page with "{{{hdr|===}}} Examine the Setup {{{hdr|===}}} #After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: <code>/home/ubuntu..."
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{{{hdr|===}}} Examine the Setup {{{hdr|===}}}

#After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: <code>/home/ubuntu</code>

## You can check this by doing:

##:<pre>pwd</pre>

##* This should output: <code>/home/ubuntu</code>

## Take a look at the contents of the ubuntu user home directory

##: <pre>ls</pre>

##* This should output be 2 directories, <code>example</code> and <code>gotcloud</code>

##** The <code>example</code> directory contains the files for this demo

##** The <code>gotcloud</code> directory contains the gotcloud programs and pre-compiled source

#:[[File:DemoHome.png|400px]]

# Look at the example input files:

#:<pre>ls example</pre>

#:[[File:ExampleFiles.png|400px]]

#:# <code>bam.list</code> contains the list of BAM files per sample

#:# <code>bams</code> is a subdirectory containing the BAM files for this demo

#:# <code>test.bed</code> 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

#:#:[[File:BedContents.png|400px]]

#:# <code>test.conf</code> contains the settings we want GotCloud to use for this run

#:#:[[File:ConfContents.png|400px]]

#:#:* For the demo, we want to tell GotCloud:

#:#:*# The list of bams to use: <code>BAM_LIST = example/bam.list</code>

#:#:*# The region to process rather than the whole genome: <code>UNIFORM_TARGET_BED = example/test.bed</code>

#:#:*# The chromosomes to process.  The default chromosomes are 1-22 & X, but we only want to process chromosome 22: <code>CHRS = 22</code>

Template:GotCloud: Amazon Demo Setup - Revision history

Mktrost: Mktrost moved page GotCloud: Amazon Demo Setup to Template:GotCloud: Amazon Demo Setup

Mktrost: Created page with "{{{hdr|===}}} Examine the Setup {{{hdr|===}}} #After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: /home/ubuntu..."

Mktrost: Created page with "{{{hdr|===}}} Examine the Setup {{{hdr|===}}} #After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: `/home/ubuntu..."`