grid-computing-tools

The grid-computing-tools repo is intended to be a place for scripts and recipes for solving some very common issues, which typically fall under the category of "simple for a few files, hard for many files." Examples include:

• I have many VCFs in Cloud Storage that I need to (de)compress
• I have many VCFs in Cloud Storage that have something wrong with the header
• I have many BAMs in Cloud Storage for which I need to compute index files

grid-computing-tools components

The primary components of the grid-computing-tools examples are:

• Google Cloud Storage - location of source input files and destination for output files
• Google Compute Engine - virtual machines in the cloud
• Grid Engine - job scheduling software to distribute commands across a cluster of virtual machines

The approach here is intended to provide a familiar environment to computational scientists who are accustomed to using Grid Engine to submit jobs to fixed-size clusters available at their research institution.

Available Tools

Documentation for the tools in this repo can be found at http://googlegenomics.readthedocs.org/

The following tools are available:

• Compress/Decompress files in Google Cloud Storage
• With SAMtools index BAM files in Google Cloud Storage