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broadinstitute
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gdctools
Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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Cli flags
#39
noblem
closed
7 years ago
0
synonyms and other CLI simplification & rationalization
#38
noblem
opened
7 years ago
2
Fixed OV test failures and added back to test suite. Corrected bug in download retries. Files that cause an error during download are removed to avoid conflict.
#37
dheiman
closed
7 years ago
1
If curl call fails during mirror (e.g. due to timeout) the partially downloaded file needs to be removed
#36
dheiman
closed
7 years ago
1
Minor code cleanup - define fixed data structures outside of functions, remove redundancy, better follow python conventions.
#35
dheiman
closed
7 years ago
0
Updated repo to work with Python3. Included support for direct virtua…
#34
sammeier
closed
7 years ago
2
move tests/diff/bdiff.py to util directory
#33
noblem
closed
7 years ago
1
calls to requests library should be using session object
#32
noblem
opened
7 years ago
0
Move and update counting
#31
dheiman
closed
7 years ago
0
Minor errors in various files
#30
aswanipranjal
closed
7 years ago
6
How to retrieve data from GDC using Python API
#29
fbrundu
opened
7 years ago
3
Move and update counting
#28
dheiman
closed
7 years ago
4
Move and update counting
#27
dheiman
closed
7 years ago
1
would be helpful if gdc_list could enumerate fields and permissible values
#26
noblem
opened
7 years ago
0
Move heatmap generation to reports
#25
dheiman
closed
7 years ago
0
files/cases needs to be accessible by UUID, too
#24
noblem
opened
7 years ago
0
GDCtools should give user option of employing GDC data transfer tool
#23
noblem
opened
7 years ago
0
Add edge case testing for invalid --programs and --project values
#22
noblem
closed
6 years ago
1
MAF counting is very broken
#21
noblem
closed
7 years ago
0
draw_heatmaps should be moved from gdc_dice to gdc_report
#20
noblem
closed
7 years ago
0
sample report should accept title argument at runtime
#19
noblem
opened
7 years ago
0
test_report failure
#18
noblem
closed
7 years ago
0
gdc_list should not support the full set of CLI flags that gdc_mirror, dice etc do
#17
noblem
closed
7 years ago
1
Content for WIKI
#16
noblem
opened
7 years ago
0
investigate whether GDC api spec can be converted to OpenAPI (Swagger2 / YAML)
#15
noblem
opened
7 years ago
0
consider partitioning gdc_mirror into 2 tools: one to retrieve manifest, one to retrieve files
#14
noblem
opened
7 years ago
0
Helpful error & usage messages for CLI tools
#13
tmdefreitas
closed
6 years ago
1
Cannot run tools standalone (i.e. outside of repo directory)
#12
noblem
closed
7 years ago
2
tests: we should use vastly smaller subset of data for testing
#11
noblem
closed
7 years ago
1
tests: mirror/dice/report actions are performed but not validated
#10
noblem
closed
7 years ago
3
Nothing mirrored, but dicing still kicked off
#9
noblem
closed
7 years ago
2
Mirror/Dice version stamp out of sync?
#8
noblem
closed
7 years ago
0
version stamp used in sample_report: RFE
#7
noblem
closed
7 years ago
0
non-existent config file should throw error
#6
noblem
closed
7 years ago
0
tests make it clear that we need a --cases option to select subset of available cases
#5
noblem
closed
7 years ago
1
logging should go into GDCtool base class
#4
noblem
closed
7 years ago
2
create_loadfile and matplotlib dependency
#3
noblem
closed
7 years ago
1
Bad --programs and --projects options should fail immediately
#2
noblem
closed
7 years ago
2
reconcile --projects and --programs options with config file content
#1
noblem
closed
7 years ago
0
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