Difference between revisions of "GotCloud"
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*Alignment | *Alignment | ||
*Variant Calling | *Variant Calling | ||
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| + | It Connects sequence analysis tools in an automated pipeline | ||
Key Features: | Key Features: | ||
*Scalable to tens of thousands of samples | *Scalable to tens of thousands of samples | ||
| Line 13: | Line 15: | ||
*Available via Debian Packages | *Available via Debian Packages | ||
| + | Takes pipelines we have been using for our sequence data processing and makes them publicly available & usable. | ||
The following describes the use of this software with the Amazon Web Services (https://aws.amazon.com/), | The following describes the use of this software with the Amazon Web Services (https://aws.amazon.com/), | ||
| Line 18: | Line 21: | ||
Latest Documentation at [[Tutorial: GotCloud]] | Latest Documentation at [[Tutorial: GotCloud]] | ||
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== Join GotCloud mailing list == | == Join GotCloud mailing list == | ||
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You can also email Mary Kate Wing (mktrost@umich.edu). | You can also email Mary Kate Wing (mktrost@umich.edu). | ||
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| + | |||
| + | == Detailed Background Information == | ||
| + | |||
| + | *Why use GotCloud? | ||
| + | ** Many tools required to create high quality | ||
| + | |||
| + | [[File:GotCloudDiagram.png]] | ||
| + | |||
== Setup == | == Setup == | ||
Revision as of 18:02, 8 March 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:
- Alignment
- Variant Calling
It Connects sequence analysis tools in an automated pipeline 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
Takes pipelines we have been using for our sequence data processing and makes them publicly available & usable.
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.
Latest Documentation at Tutorial: GotCloud
Join GotCloud mailing list
Please join in the GotCloud Google Group to ask / discuss / comment about these pipelines.
Currently the "join" button appears to be missing. Click "NEW TOPIC", then select "Join this group". You can then cancel the message post (or post a message).
You can also email Mary Kate Wing (mktrost@umich.edu).
Detailed Background Information
- Why use GotCloud?
- Many tools required to create high quality
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.
