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 . |
| | | |
− | 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 steps in the GotCloud pipeline: | + | 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 that ought to be hidden or deleted: | + | 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 |