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, 09:58, 17 October 2014
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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: |
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| #:#:*# 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]] |