Talk:GotCloud: Difference between revisions
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The main page is http://genome.sph.umich.edu/wiki/GotCloud . | The main page is http://genome.sph.umich.edu/wiki/GotCloud . | ||
Pages that document or help with installation: | |||
* http://genome.sph.umich.edu/wiki/GotCloud:_Binary_Releases | * 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:_Source_Releases | ||
| Line 12: | Line 12: | ||
** http://genome.sph.umich.edu/wiki/StarCluster | ** http://genome.sph.umich.edu/wiki/StarCluster | ||
Pages that document 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 (sub-page) | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_GenomeSTRiP_Pipeline | |||
* http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline | |||
Pages that document 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 | ||
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* 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) | ||
Pages that explain configuration: | |||
* http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers <code>BATCH_OPTS</code>) | * http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers <code>BATCH_OPTS</code>) | ||
| Line 37: | Line 39: | ||
Pages for developers: | Pages for developers: | ||
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud | * http://genome.sph.umich.edu/wiki/Releasing_GotCloud | ||
* http://genome.sph.umich.edu/wiki/Git_FAQs | |||
* http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2 | * http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2 | ||
Other: | Other pages: | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_FAQs | * http://genome.sph.umich.edu/wiki/GotCloud:_FAQs | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions | * http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions | ||
Latest revision as of 16:40, 1 April 2016
Organization of the GotCloud pages on this wiki
The main page is http://genome.sph.umich.edu/wiki/GotCloud .
Pages that document or help with installation:
- 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
Pages that document 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:_GenomeSTRiP_Pipeline
- http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline
Pages that document 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)
Pages that explain 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/Git_FAQs
- http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2
Other pages:
- 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
