Docs

For GMS users

Examples of input and output files

Location and description of HCC1395 WGS, Exome, and RNA-seq data
Important results files in GMS builds

Detailed descriptions of GMS Pipelines

Reference Alignment
Somatic Variation
RnaSeq
Differential Expression
Genotype Microarray
Clinical Sequencing
Post processing of Somatic Variation Models

Miscellaneous

Storage required for various test analyses
The GMS compared to conceptually related resources
Importing auxillary data such as references, annotations, etc.
Working with GMS virtual machines
Expanding the GMS to multiple nodes
How do I clean up an orphaned allocation?

For GMS developers

Developer's guide to installing the GMS on an AWS instance
AWS Developer Notes
Developer's guide to installing the GMS on an OpenStack instance
General documentation for GMS developers in the 'genome' group
How software gets installed in the sGMS
Succesful software configurations
Git repos and branches
Where are resource requests (cpus, mem, tmp space) defined for major compute steps?
How is the APT repo that the sGMS installs from created ?
Writing a New Command Class in the Genome Modeling System
Adding a Result to the ClinSeq Pipeline
Using the Genome/UR Class Browser