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Important Directories
DirectoryDescription
/xchip/tcga/Tools/gdac/binAdd this to your $PATH–it houses the GDAC OPS production toolchain, and numerous other tools authored by the GDAC (including fiss, firehose_get, hydrant, fbget, MongoDB utilities, etc)
/xchip/gdac_data

Our main disk: for both internal operations and public-facing website.

/xchip/gdac_data/.zfs/snapshot

Snapshot backups of our main disk. Note that you MUST change into the .zfs directory in order to view its content. You WILL NOT be able to see .zfs from the root of /xchip/gdac_data with the expected "ls -la" Unix command. Usage can also be "monitor"-ed via the IT storage appliance GUI (contact Mike Noble for password)

/xchip/gdac_data/runsGDAC run dashboards: corresponds to this public facing runs URL

/xchip/gdac_data/gdc/mirror

/xchip/gdac_data/dcc_mirror3

Root directory of GDAN mirror tree (taking data from Genomic Data Commons).

Root directory of our legacy TCGA mirroring tree (DCC is no longer active).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

/web/webcluster/logs/gdac

Log files for our website, useful e.g. to monitor usage traffice (page views, bandwidth, etc), as well HTML 404 errors in our reports, etc

/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)

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