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firehose_get v0.3.5


Retrieving or utilizing TCGA results need not be difficult, especially for open-access data.  To help simplify, we're currently beta-testing the firehose_get retrieval script.  To join our beta effort, simply download the zip file from here, perform these 2 steps from a Unix-compatible command line

        unix%   unzip firehose_get.zip
  unix%  ./firehose_get 

and follow the instructions (excerpted below).  Please note that downloading data from our site constitutes agreement to this data usage policy.  If you are missing wget, please look here for links to pre-built versions for your system.

firehose_get : retrieve open-access results of Broad Institute TCGA GDAC runs
Version: 0.3.5 (Author: Michael S. Noble)

Usage: firehose_get [flags]  RunType  Date  [tumor_type, ... ]

Two arguments are required; the first must be one of

    analyses
    awg_pancan8
    stddata

while the second must EITHER be a date (in YYYY_MM_DD form) of an
existing GDAC run of the given type OR 'latest'.  An optional third,
fourth etc argument may be specified to prune the retrieval, given
as a subset of these case-insensitive TCGA tumor type abbreviations:

  BLCA BRCA CESC COADREAD DLBC GBM HNSC KICH KIRC KIRP LAML LGG
  LIHC LUAD LUSC OV PAAD PRAD SARC SKCM STAD THCA UCEC PANCANCER

Note that as a convenience 'analysis' and 'data' are accepted as
synonyms for the 'analyses' and 'stddata' run types

Flags:

  -b | -batch              do not prompt: assume YES answer to all queries
  -e | -echo               show commands that would be run, but do nothing
  -h | -help | --help    this message
  -l | -log                   write output to log file, instead of stdout
  -r | -runs                display list of all available Firehose runs
  -t | -tasks <list>      further prune the set of archives retrieved, by
                                INCLUDING only the tasks (pipelines) whose
                                names match the given space-delimited list of
                                patterns; matching is performed with glob-style
                                wildcards; if a tilde ~ is prepended to a task
                               name then matching tasks will be EXCLUDED; when
                               no pattern list is given firehose_get will display
                               all tasks in the selected run

                               NOTE: not all tasks will execute for all tumor
                               sets; what tasks are run depends upon the
                               data available for that tumor type


  -v                          display the version of firehose_get
  -x                          debugging: turn on bash set -x (warning: very verbose)

For more information see the Broad GDAC website or send an email to
          http://gdac.broadinstitute.org
          gdac@broadinstitute.org

 Copyright and Disclaimer
#===============================================================================
# This software and its documentation are copyright 2012 by the
# Broad Institute/Massachusetts Institute of Technology. All rights reserved.
#
# This software is supplied without any warranty or guaranteed support whatsoever.
# Neither the Broad Institute nor MIT can be responsible for its use, misuse, or
# functionality.
#===============================================================================
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