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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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Clinical dicing update
#89
dheiman
closed
5 years ago
1
loadfiles need to contain unadulterated case id
#88
noblem
opened
6 years ago
0
Merge CPTAC support code into master branch
#87
noblem
closed
6 years ago
0
annotation_table enhancement: stop using Firehose_annotation column name
#86
noblem
opened
6 years ago
0
findPython.sh should prioritize an activated virtual environment over all else
#85
dheiman
closed
6 years ago
1
gdc_report should tolerate missing filter file
#84
noblem
opened
6 years ago
0
need to cross-check samples for consistency
#83
noblem
opened
6 years ago
1
Support new V2 segfile, and externalize test data for simpler/faster builds
#82
noblem
closed
6 years ago
0
simplify & rationalize dicing of [new] data types
#81
noblem
opened
6 years ago
0
change when ingestor syncs data & writes VERSION to cloud
#80
noblem
opened
6 years ago
0
regression tests need to be less dependent upon content of data at GDC
#79
noblem
opened
6 years ago
0
sample reports should be segregated by "program" name
#78
noblem
opened
6 years ago
1
logfiles should be segregated by "program" name
#77
noblem
opened
6 years ago
1
problem dicing latest CN data (from 2018_06_13)
#76
noblem
closed
6 years ago
1
Failed to mirror TCGA-BRCA
#75
buchanae
closed
6 years ago
2
exclude tests directory when doing pip install
#74
noblem
opened
6 years ago
1
Improve config file to support exclusion of data types during mirror
#73
noblem
opened
6 years ago
0
generalize sample reports
#72
noblem
opened
6 years ago
1
Pull in master v0.2.6.7: ensuring that config and reference files are installed; updat…
#71
noblem
closed
6 years ago
0
major bug: reference files not installed
#70
noblem
closed
6 years ago
1
RFE: small tweaks to summarization
#69
noblem
opened
6 years ago
0
New maf datatypes need to be recognized
#68
gsaksena
opened
6 years ago
3
Gsaksena mmd2
#67
gsaksena
opened
6 years ago
15
gdc_loadfile v0.3.5
#66
dheiman
closed
6 years ago
1
gdac_loadfile allowed FFPE samples into a -TP sampleset
#65
gsaksena
closed
6 years ago
5
BUG: multiple versions of clustering algorithms showing up in reports
#64
noblem
closed
6 years ago
0
RFE: tools should be more stringent about when nothing needs to be done
#63
noblem
opened
6 years ago
0
RFE: facilitate operation of downstream tools in offline mode
#62
noblem
opened
6 years ago
0
Loadfile format
#61
noblem
closed
6 years ago
0
python3 test failing, due to code from methylation branch
#60
noblem
closed
6 years ago
1
Replicates test
#59
noblem
closed
6 years ago
0
Some tools do not return proper exit code to invocation context (e.g. shell)
#58
noblem
closed
6 years ago
1
gdc_loadfile does not observe or respect datestamps properly
#57
noblem
closed
6 years ago
2
Cohorts include program name consistently (program-project)
#56
dheiman
closed
6 years ago
0
Scrub code to remove TCGA specificity
#55
noblem
opened
6 years ago
2
sample counts table needs to include project in cohort name
#54
noblem
closed
6 years ago
2
gdc_mirror reports success even when some downloads fail
#53
gsaksena
opened
7 years ago
3
gdc_loadfile is not preserving file paths
#52
dheiman
closed
6 years ago
2
RFE: enable use of FORMAT argument in gdc_loadfile
#51
dheiman
closed
6 years ago
1
docs need to be explicit about how configuration works: cli flags, config files, defaults ...
#50
noblem
closed
6 years ago
1
fragility: gdc_report looks for config/blacklist.tsv (per tcga.cfg) ...
#49
noblem
opened
7 years ago
0
gdc_loadfile sometimes does nothing
#48
gsaksena
closed
6 years ago
2
behavior surprise when gdc_dice follows multiple gdc_mirror calls
#47
gsaksena
opened
7 years ago
9
fix edge cases in config file handling
#46
noblem
closed
7 years ago
3
New types of SNV data at GDC: needs scrutiny
#45
noblem
closed
7 years ago
2
soft timeout when mirroring methylation data
#44
gsaksena
opened
7 years ago
0
BUG: update gdac_ingestor to reflect latest incarnation of GDCtools
#43
noblem
closed
7 years ago
1
possible bug in diced_file_comparator
#42
cbirger
closed
7 years ago
2
Gsaksena methyl
#41
gsaksena
closed
7 years ago
4
dicer does not handle failures appropriately
#40
noblem
opened
7 years ago
0
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