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== Running the Demo on Already Running Node ==
== Running the Demo on Already Running Node ==
=== Examine the 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>
#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:
## You can check this by doing:
#:#:*# The region to process rather than the whole genome: <code>UNIFORM_TARGET_BED = example/test.bed</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>
#:#:*# The chromosomes to process. The default chromosomes are 1-22 & X, but we only want to process chromosome 22: <code>CHRS = 22</code>
=== Run GotCloud SnpCall ===
Now that we have examined the instance files, run GotCloud snpcall
# <pre>gotcloud snpcall --conf example/test.conf --outdir output --numjobs 8</pre>
#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
#: [[File:RunSnpCall.png|700px]]
#:* This will take a few minutes to run.
#:* GotCloud first generates a makefile, and then runs the makefile
#:* After a while GotCloud snpcall will print some messages to the screen. This is expected and ok.
# When complete, GotCloud snpcall will indicate success/failure
#:[[File:SnpcallSuccess.png]]
