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firehose_get   version 0.4.

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11 (released

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2017_

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10_

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10)

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Please note that downloading data from the Broad TCGA GDAC site constitutes agreement to this data usage policy.

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Expand
titleChange Log
No Format
v0.4.10:
    Enable download of .zip files from Firecloud runs
v0.4.9: 2017_08_22
    Patch submitted by gennady.margolin@nih.gov, to ensure post-processing
    completes even when dirnames contain spaces
v0.4.8: 2016_11_17:
	    Support new GDC-style names for TCGA disease cohorts, which prepend TCGA-
	    to the name; e.g. the ACC cohort in legacy TCGA becomes TCGA-ACC in GDC.
	    This applies to all runs conducted after 2016_07_15, the formal end date
	    of TCGA.
0.4.7: 2016_09_28
	    Make tool slightly friendlier by filtering out more uninformative noise
	    from wget, while iterating through downloads
v0.4.6: 2016_05_18
    firehose_get was originally developed on an ancient CentOS Linux system,
    but since then newer OS versions have become more stringent in enforcing
    security protocols; this release acknowledges that by referencing the
    GDAC site url as https:// instead of http://
v0.4.5: 2015_09_01
    Nicer feedback when some runs do not include data/results for all cohorts
v0.4.4: 2015_01_23
    When PANCAN12 was discontinued as a cohort, it broke -tasks listing here,
    so use THCA cohort instead
v0.4.3: 2013_11_08
    When possible, output better diagnostic message for wget errors
v0.4.2:     2013_09_26
    bugfix: recent edits broke -tasks list when run for "all" disease cohorts
0.4.1:      2013_09_03
    Turn off 'set -o pipefail' while ascertaining which downloader to employ,
    to better inform users when wget/etc cannot be found in $PATH
v0.4.0:     2013_08_25
    introduce -auth option, for retrieval of password protected (e.g. AWG) runs
v0.3.13:    2013_06_24
    introduce -only option, as clearer equivalent to -tasks
v0.3.12:    2013_06_04
    perform round trip to GDAC site less to determine valid run type/date
    warn user earlier when input does not map to an existing GDAC firehose run
    give "kinder" feedback when nothing was downloaded
v0.3.11:    2013_02_14
    help output is now shorter by default, when no args given
    -tasks flag now case insensitive
    tiny clarifications & improvements to help docs
v0.3.10:    2013_01_31
   remove hardcoded disease names, in favor of downloading from Broad site
   enhanced firehose_get_scan output (as was done for -runs below)
v0.3.9:     2012_12_22
   use firehose_get_scan tool (on Broad servers), and download its output
   to client sites, to speed up discovery for -runs flag, etc
v0.3.8:     2012_11_16
   support potentially any AWG with generic awg_<disease> run type
v0.3.7:     2012_10_21
   support PANCAN8 analysis working group (AWG) runs
v0.3.6:     2012_09_20
   -runs considers ONLY those GDAC runs with ./data subdir
v0.3.5:     2012_09_12
   discontinue use of static run lists, in favor of dynamically querying GDAC
                site to display list of runs, what kinds of runs, etc
    support EXCLUDE in -tasks with tilde/~ prefix
v0.3.4:     2012_09_07
    tweak date regex to correctly detect October months
v0.3.3:     2012_07_12
    fix printf msg emitted when nothing downloaded
    employ --cache=off, so that most up-to-date run lists are always retrieved
v0.3.2:     2012_06_08
    added -b/-batch for headless use
    'latest' now translated to date prior to download
    be less compulsive when cleaning up
v0.3.1:     2012_05_02
    accept --version, too
    use tumor types to subset list of tasks returned, too
    warn user when subsetted runs return nothing for the given tumor(s)
v0.3.0:     2012_04_22
    tweak awkward wording of -tasks help
    allow --help, too
    -runs flag to display list of available runs
    -tasks flag to subset by glob-pattern matching against task names

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