Difference between revisions of "Talk:GotCloud"
From Genome Analysis Wiki
Jump to navigationJump to search| (3 intermediate revisions by the same user not shown) | |||
| Line 3: | Line 3: | ||
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:_GenomeSTRiP_Pipeline | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_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 | ||
| Line 29: | Line 29: | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions) | * 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 40: | 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
