v0.4.11 & 0.4.12:
Enable retrieval of GDAN internal runs from 2017_09_19 and 2018_01_18
(requires GDAN awg credentials)
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 |