Difference between revisions of "GotCloud"
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Details for the Choices of Your Install | Details for the Choices of Your Install | ||
| − | * | + | === Install GotCloud Software === |
| − | * | + | * As a [[Pipeline Debian Package|debian package]] |
| + | * As a [[Pipeline RedHatPackage|red hat package]] | ||
| + | * As a tar | ||
| + | * On Amazon EC2 | ||
| + | ** Create a volume using our [[Amazon Snapshot]] | ||
| + | ** Create an EC2 cluster instance using [[StarCluster|StarCluster]] | ||
| + | |||
| + | === Install Resource Files === | ||
* Install [[Genetic Reference and Resource Files|genetic resource files]] | * Install [[Genetic Reference and Resource Files|genetic resource files]] | ||
| − | |||
| − | |||
| − | |||
'''Resources / Cost''' | '''Resources / Cost''' | ||
| + | * [[AWS Resources|AWS Resources]] | ||
| − | * [[ | + | === Configure === |
| + | * [[Configure GotCloud|Configure Gotcloud]] for your installation | ||
| − | |||
| − | |||
| − | |||
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| − | |||
| − | |||
== Running GotCloud Software == | == Running GotCloud Software == | ||
* [[Mapping Pipeline]] | * [[Mapping Pipeline]] | ||
| + | ** | ||
* [[Variant Calling Pipeline (UMAKE)]] | * [[Variant Calling Pipeline (UMAKE)]] | ||
| + | |||
| + | |||
| + | == Development Notes == | ||
| + | * [[Creating Packages]] | ||
| + | * Amazon EC2 | ||
| + | ** [[Creating a Snapshot on EC2]] | ||
| + | ** [[Creating an AMI on EC2]] | ||
| + | ** [[Mount S3 Volume]] | ||
| + | ** Notes on sequence data preparation in [[Amazon Storage|Amazon Storage]]. | ||
Revision as of 23:07, 20 February 2013
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) for:
- Mapping
- Variant Calling
Key Features:
- Scalable to tens of thousands of samples
- Robust against unexpected system failure using GNU make
- Massively parallel, can run hundreds of jobs
- Easy to use - Automates series of configurable steps
- Available on Amazon Web Services (AWS) Elastic Compute Cloud (EC2)
- Run on local machines/clusters
- Available via Debian Packages
The following describes the use of this software with the Amazon Web Services (https://aws.amazon.com/),
but you can just as easily use the pipelines on your own machine(s) by just installing them.
Join in GotCloud mailing list
Please join in the GotCloud Google Group to ask / discuss / comment about these pipelines.
Setup
You may run the GotCloud software in several modes:
- On your own hardware running Ubuntu or Redhat/CentOS. See the instructions about installing the software below.
- On any EC2 instance that uses Ubuntu or Redhat/CentOS distribution. You can install the software as described below, or create a volume using our snapshot (see Amazon Snapshot).
- On an EC2 cluster instance created by StarCluster. You can install the software as described below, or create a volume using our snapshot (see Amazon Snapshot).
Details for the Choices of Your Install
Install GotCloud Software
- As a debian package
- As a red hat package
- As a tar
- On Amazon EC2
- Create a volume using our Amazon Snapshot
- Create an EC2 cluster instance using StarCluster
Install Resource Files
- Install genetic resource files
Resources / Cost
Configure
- Configure Gotcloud for your installation
Running GotCloud Software
Development Notes
- Creating Packages
- Amazon EC2
- Creating a Snapshot on EC2
- Creating an AMI on EC2
- Mount S3 Volume
- Notes on sequence data preparation in Amazon Storage.
