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= Genomes on the Cloud (GotCloud) Introduction=
== Genomes on the Cloud (GotCloud) Introduction==
To handle the increasing volume of next generation sequencing and genotyping data, we created and developed software pipelines called '''Genomes on the Cloud (GotCloud).'''
To handle the increasing volume of next generation sequencing and genotyping data, we created and developed software pipelines called '''Genomes on the Cloud (GotCloud).'''
[[File:Gotcloud.puzzles.v2.png|500px]]
[[File:Gotcloud.puzzles.v2.png|500px]]
== Getting Help with GotCloud ==
=== Getting Help with GotCloud ===
Please join in the [http://groups.google.com/group/GotCloud GotCloud Google Group] to ask / discuss / comment about these pipelines.
Please join in the [http://groups.google.com/group/GotCloud GotCloud Google Group] to ask / discuss / comment about these pipelines.
== Sequence Analysis Background Information ==
=== Sequence Analysis Background Information ===
There are many essential steps in the analysis of next generation sequence data.
There are many essential steps in the analysis of next generation sequence data.
[[File:GotCloudDiagram.jpg|500px]]
[[File:GotCloudDiagram.jpg|500px]]
= GotCloud Setup =
== GotCloud Setup ==
You may run the GotCloud software in several modes:
You may run the GotCloud software in several modes:
GotCloud has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested.
GotCloud has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested.
== GotCloud Dependencies ==
=== GotCloud on Amazon ===
You can take advantage of GotCloud AMI's when running on Amazon. The GotCloud already includes GotCloud and default reference files.
See [[GotCloud: Amazon]] for instructions on using GotCloud on Amazon.
=== GotCloud Dependencies ===
GotCloud requires certain things to be installed in order to run:
GotCloud requires certain things to be installed in order to run:
[gotcloud_path]/scripts/check_requirements.sh
[gotcloud_path]/scripts/check_requirements.sh
== Install GotCloud Software ==
=== Install GotCloud Software ===
You can install gotCloud on your system as (follow the links for the appropriate instructions):
You can install gotCloud on your system as (follow the links for the appropriate instructions):
For more information on Amazon Web Services, see: https://aws.amazon.com/
For more information on Amazon Web Services, see: https://aws.amazon.com/
== GotCloud Reference/Resource Files ==
=== GotCloud Reference/Resource Files ===
In order to run gotCloud, you need to provide Genetic Reference and Resource Files.
In order to run gotCloud, you need to provide Genetic Reference and Resource Files.
* When running on Amazon, a default set of reference files are included in the GotCloud AMI.
* When running on Amazon, a default set of reference files are included in the GotCloud AMI.
== Configure GotCloud ==
=== Configure GotCloud ===
* [[Configure GotCloud|Configure Gotcloud]] for your installation
* [[Configure GotCloud|Configure Gotcloud]] for your installation
