GotCloud: Amazon Demo
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Revision as of 09:58, 17 October 2014 by Mktrost (talk | contribs) (→Running the Demo on Already Running Node)
Introduction
This Amazon demo runs through the GotCloud SNP and INDEL calling pipelines.
The data used for this demo is originally from our sequencing workshop demos. We also have alignment and structural variation demos.
Links to the general GotCloud Demos (originally from our sequencing workshop):
- SeqShop: Sequence Mapping and Assembly Practical
- SeqShop: Variant Calling and Filtering for SNPs Practical
- SeqShop: Variant Calling and Filtering for INDELs Practical
- SeqShop: Analysis of Structural Variation Practical
Starting up a Node
See Amazon Single Node for instructions on starting a node and getting a terminal running.
- For the demo, we recommend using a
c3.2xlarge
instance.
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:
/home/ubuntu
- You can check this by doing:
pwd
- This should output:
/home/ubuntu
- Take a look at the contents of the ubuntu user home directory
ls
- This should output be 2 directories,
example
and
gotcloud
- The
example
directory contains the files for this demo - The
gotcloud
directory contains the gotcloud programs and pre-compiled source
- The
- You can check this by doing:
- Look at the example input files:
ls example
-
bam.list
contains the list of BAM files per samplebams
is a subdirectory containing the BAM files for this demotest.bed
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
test.conf
contains the settings we want GotCloud to use for this run-
- For the demo, we want to tell GotCloud:
- The list of bams to use:
BAM_LIST = example/bam.list
- The region to process rather than the whole genome:
UNIFORM_TARGET_BED = example/test.bed
- The chromosomes to process. The default chromosomes are 1-22 & X, but we only want to process chromosome 22:
CHRS = 22
- The list of bams to use:
- For the demo, we want to tell GotCloud:
-
Run GotCloud SnpCall
Now that we have examined the instance files, run GotCloud snpcall
gotcloud snpcall --conf example/test.conf --outdir output --numjobs 8
- 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
- When complete, GotCloud snpcall will indicate success/failure