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 . | ||
Setup instructions: | Setup instructions and documentation: | ||
* 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 | ||
Documentation of | Documentation of pieces of GotCloud: | ||
* 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) | ||
* 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:_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/PileupBasedVariantCalling | |||
* http://genome.sph.umich.edu/wiki/GotCloud:_Filters | * 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:_GenomeSTRiP_Pipeline | |||
* http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline | |||
Configuration: | Configuration: | ||
| Line 24: | Line 32: | ||
Tutorials: | Tutorials: | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo | * 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: | 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/Creating_an_AMI_on_EC2 | * 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: | Event-specific pages: | ||
* http://genome.sph.umich.edu/wiki/Short_Workshops lists all of these | |||
* http://genome.sph.umich.edu/wiki/SeqShop:_May_2015 (and sub-pages) | |||
* http://genome.sph.umich.edu/wiki/SeqShop:_December_2014 (and sub-pages) | |||
* http://genome.sph.umich.edu/wiki/SeqShop:_June_2014 (and sub-pages) | |||
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG | * http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG | ||
* http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM | * http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM | ||
| Line 37: | Line 55: | ||
** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8 | ** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8 | ||
Pages | 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/GotCloud:_RedHat_Package | ||
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud | * http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud | ||
| Line 44: | Line 62: | ||
* http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2 | * http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2 | ||
* http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (<code>FA_REF</code> has since been renamed.) | * http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (<code>FA_REF</code> has 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 | |||
Revision as of 00:17, 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 pieces of GotCloud:
- http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions)
- 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/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:_GenomeSTRiP_Pipeline
- http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline
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 lists all of these
- http://genome.sph.umich.edu/wiki/SeqShop:_May_2015 (and sub-pages)
- http://genome.sph.umich.edu/wiki/SeqShop:_December_2014 (and sub-pages)
- http://genome.sph.umich.edu/wiki/SeqShop:_June_2014 (and sub-pages)
- http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG
- http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM
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
