Difference between revisions of "Talk:GotCloud"
From Genome Analysis Wiki
Jump to navigationJump to search| Line 12: | Line 12: | ||
** http://genome.sph.umich.edu/wiki/StarCluster | ** http://genome.sph.umich.edu/wiki/StarCluster | ||
| − | Documentation of | + | Documentation of steps in the GotCloud pipeline: |
| − | |||
* http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline | * http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline | ||
** http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Sub-Pipelines | ** http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Sub-Pipelines | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline | * http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options | * http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options | ||
| + | * http://genome.sph.umich.edu/wiki/GotCloud:_GenomeSTRiP_Pipeline | ||
| + | * http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline | ||
| + | |||
| + | Documentation of pieces of GotCloud: | ||
* http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling | * http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Filters | * http://genome.sph.umich.edu/wiki/GotCloud:_Filters | ||
| Line 24: | Line 27: | ||
* http://genome.sph.umich.edu/wiki/Understanding_QPLOT_output | * http://genome.sph.umich.edu/wiki/Understanding_QPLOT_output | ||
* http://genome.sph.umich.edu/wiki/Understanding_vcf-summary_output | * http://genome.sph.umich.edu/wiki/Understanding_vcf-summary_output | ||
| − | * http://genome.sph.umich.edu/wiki/GotCloud: | + | * http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions) |
| − | + | ||
Configuration: | Configuration: | ||
Revision as of 00:21, 8 January 2016
Organization of the GotCloud pages on this wiki
The main page is http://genome.sph.umich.edu/wiki/GotCloud .
Setup instructions and documentation:
- http://genome.sph.umich.edu/wiki/GotCloud:_Binary_Releases
- http://genome.sph.umich.edu/wiki/GotCloud:_Source_Releases
- http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files
- http://genome.sph.umich.edu/wiki/AWS_Resources
Documentation of steps in the GotCloud pipeline:
- http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline
- http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline
- http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options
- http://genome.sph.umich.edu/wiki/GotCloud:_GenomeSTRiP_Pipeline
- http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline
Documentation of pieces of GotCloud:
- http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling
- http://genome.sph.umich.edu/wiki/GotCloud:_Filters
- http://genome.sph.umich.edu/wiki/VcfCooker
- http://genome.sph.umich.edu/wiki/Understanding_VerifyBamID_output
- http://genome.sph.umich.edu/wiki/Understanding_QPLOT_output
- http://genome.sph.umich.edu/wiki/Understanding_vcf-summary_output
- http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions)
Configuration:
- http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers
BATCH_OPTS)
Tutorials:
- http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo
- http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo_Setup
- http://genome.sph.umich.edu/wiki/Tutorial:_Low_Pass_Sequence_Analysis
Pages for developers:
- http://genome.sph.umich.edu/wiki/Releasing_GotCloud
- http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2
Other:
- http://genome.sph.umich.edu/wiki/GotCloud:_FAQs
- http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions
Event-specific pages:
- http://genome.sph.umich.edu/wiki/Short_Workshops links to all of them (or their parents)
Pages of which some ought to be hidden, deleted, or heavily re-worked:
- http://genome.sph.umich.edu/wiki/GotCloud:_RedHat_Package
- http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud
- http://genome.sph.umich.edu/wiki/AWS_Resources
- http://genome.sph.umich.edu/wiki/Amazon_Snapshot
- http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2
- http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (
FA_REFhas since been renamed.) - http://genome.sph.umich.edu/wiki/UMAKE
- http://genome.sph.umich.edu/wiki/Mount_S3_Volume
- http://genome.sph.umich.edu/wiki/GotCloud:_AMIs
- http://genome.sph.umich.edu/wiki/GBR60vc.conf
