This page is the graveyard of content from the GDAC "Internal" page that is no longer relevant, because it applied mainly to the Legacy TCGA phase of our GDAC. It's being kept here, rather than thrown away, just in case. To lessen confusion, our aim is that no content be duplicated, i.e. each piece of content on the Internal page will either (a) remain there or (b) be moved here.

DirectoryDescription
  

/xchip/gdac_data/dcc_mirror3

Root directory of our legacy TCGA mirroring tree (DCC is no longer active).

.../platform_link/other/gdacs/gdacbroadLocation to which our FH results are mirrored: corresponds to this URL at DCC
/xchip/cga/reference/tcga

Top level of tree which contains static-ish "reference data" for FH tasks: manually curated, or culled from external sources, but NOT fed from GDAC ingestor OR generated at runtime by GDAC FH tasks at. Some examples of the kinds of data we store in the reference tree are:

    • antibody names for RPPA annotations
    • clinical parameters per TCGA disease type
    • custom inputs for aggregation into Analyses workflow (& correlation to clinical parameters)
  

/xchip/tcga/gdac/website

Top level of gdac.broadinstitute.org
/xchip/gdac_data/dcc_mirror3/control/gdacIngestor.cfg

GDAC ingestor config file (see gdac1 cron table)

Creating a Legacy TCGA Data Freeze

Standard Runs Status Tracking

AWG Run Tracking

MAF Dashboard (related: MAF Injection)

GDAC Ingestor Dev Notes

GDAC Ingestor Blacklisting

GDAC Ingestor Data Type Removal Description

FH Entity Discussion (migration to Sample Sets)

GDAC dicing and mirroring status report

GDAC Science/OPS Meetings

CGADS Software Meetings

CGADS Brainstorming

GDAC Science Meetings

Authorship List for TCGA Papers

May 2013 TCGA F2F Ideas

Nov 2012 TCGA Symposium Ideas

Clinical data update meeting - 2015

FireCloud Feature Requests

CONSOLIDATE_MULTIPLE_BUILD_PAGES_INTO_1_WITH_NEW_JULY_2014_RECIPE

GDAC Tester

FireBrowse

iCoMut - iComutDesign.pptx

Migrating Packaging out of Firehose

GDAC Firehose Module Guidelines

Compiling and Installing Python from Scratch

Python virtualenv and GDAC tools

GDAC Python Package Testing

Module and Pipeline Continuous Integration using Bamboo

GDAC_CreateMergeDataFilesSDRF Implementors

GDAC Ingestor Testing via Mini-mirror

GDAC test data tree

Firehose Integration Testing

GDAC Front Page

Local Replication of GDC VEP Annotation Pipeline

2 February 2016

R - Beyond the Basics (just a bit)

Sam Meier

1 March 2016

Effective FireCloud Development

Tim DeFreitas

14 June 2016

Firehose to iCoMut: Pathways to Rapid Discovery

David Heiman

2 August 2016

What’s Coming in Data, Analyses and Infrastructure

Mike Noble

Revamped R & best practices Sam Meier
expression analysis in GDC eraHailei Zhang

6 September 2016

28 September 2017

Building the Digital Tower: Applying Object Oriented Programming and Functional Programming

Efficient Algorithm Development

Kane Hadley

Gordon Saksena