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Revision as of 08:37, 31 October 2014
, 08:37, 31 October 2014Created 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..."
{{{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>
#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>
