Ecosyste.ms: Issues

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GitHub / broadinstitute/gdctools issues and pull requests

#89 - Clinical dicing update

Pull Request - State: closed - Opened by dheiman about 6 years ago - 1 comment

#88 - loadfiles need to contain unadulterated case id

Issue - State: open - Opened by noblem about 6 years ago
Labels: Priority_High

#87 - Merge CPTAC support code into master branch

Pull Request - State: closed - Opened by noblem about 6 years ago

#86 - annotation_table enhancement: stop using Firehose_annotation column name

Issue - State: open - Opened by noblem about 6 years ago
Labels: Priority_Medium

#85 - findPython.sh should prioritize an activated virtual environment over all else

Issue - State: closed - Opened by dheiman over 6 years ago - 1 comment

#84 - gdc_report should tolerate missing filter file

Issue - State: open - Opened by noblem over 6 years ago
Labels: bug, Priority_High

#83 - need to cross-check samples for consistency

Issue - State: open - Opened by noblem over 6 years ago - 1 comment
Labels: enhancement, Priority_High

#81 - simplify & rationalize dicing of [new] data types

Issue - State: open - Opened by noblem over 6 years ago

#80 - change when ingestor syncs data & writes VERSION to cloud

Issue - State: open - Opened by noblem over 6 years ago

#78 - sample reports should be segregated by "program" name

Issue - State: open - Opened by noblem over 6 years ago - 1 comment

#77 - logfiles should be segregated by "program" name

Issue - State: open - Opened by noblem over 6 years ago - 1 comment

#76 - problem dicing latest CN data (from 2018_06_13)

Issue - State: closed - Opened by noblem over 6 years ago - 1 comment

#75 - Failed to mirror TCGA-BRCA

Issue - State: closed - Opened by buchanae over 6 years ago - 2 comments

#74 - exclude tests directory when doing pip install

Issue - State: open - Opened by noblem over 6 years ago - 1 comment
Labels: Priority_High

#73 - Improve config file to support exclusion of data types during mirror

Issue - State: open - Opened by noblem over 6 years ago
Labels: Priority_High

#72 - generalize sample reports

Issue - State: open - Opened by noblem over 6 years ago - 1 comment

#70 - major bug: reference files not installed

Issue - State: closed - Opened by noblem over 6 years ago - 1 comment

#69 - RFE: small tweaks to summarization

Issue - State: open - Opened by noblem almost 7 years ago

#68 - New maf datatypes need to be recognized

Issue - State: open - Opened by gsaksena about 7 years ago - 3 comments

#67 - Gsaksena mmd2

Pull Request - State: open - Opened by gsaksena about 7 years ago - 15 comments

#66 - gdc_loadfile v0.3.5

Pull Request - State: closed - Opened by dheiman about 7 years ago - 1 comment

#65 - gdac_loadfile allowed FFPE samples into a -TP sampleset

Issue - State: closed - Opened by gsaksena about 7 years ago - 5 comments

#62 - RFE: facilitate operation of downstream tools in offline mode

Issue - State: open - Opened by noblem about 7 years ago

#61 - Loadfile format

Pull Request - State: closed - Opened by noblem about 7 years ago

#60 - python3 test failing, due to code from methylation branch

Issue - State: closed - Opened by noblem about 7 years ago - 1 comment

#59 - Replicates test

Pull Request - State: closed - Opened by noblem about 7 years ago

#58 - Some tools do not return proper exit code to invocation context (e.g. shell)

Issue - State: closed - Opened by noblem about 7 years ago - 1 comment

#57 - gdc_loadfile does not observe or respect datestamps properly

Issue - State: closed - Opened by noblem about 7 years ago - 2 comments

#56 - Cohorts include program name consistently (program-project)

Pull Request - State: closed - Opened by dheiman about 7 years ago

#55 - Scrub code to remove TCGA specificity

Issue - State: open - Opened by noblem about 7 years ago - 2 comments

#54 - sample counts table needs to include project in cohort name

Issue - State: closed - Opened by noblem about 7 years ago - 2 comments

#53 - gdc_mirror reports success even when some downloads fail

Issue - State: open - Opened by gsaksena over 7 years ago - 3 comments

#52 - gdc_loadfile is not preserving file paths

Issue - State: closed - Opened by dheiman over 7 years ago - 2 comments
Labels: bug

#51 - RFE: enable use of FORMAT argument in gdc_loadfile

Issue - State: closed - Opened by dheiman over 7 years ago - 1 comment
Labels: enhancement

#48 - gdc_loadfile sometimes does nothing

Issue - State: closed - Opened by gsaksena over 7 years ago - 2 comments

#47 - behavior surprise when gdc_dice follows multiple gdc_mirror calls

Issue - State: open - Opened by gsaksena over 7 years ago - 9 comments

#46 - fix edge cases in config file handling

Issue - State: closed - Opened by noblem over 7 years ago - 3 comments

#45 - New types of SNV data at GDC: needs scrutiny

Issue - State: closed - Opened by noblem over 7 years ago - 2 comments

#44 - soft timeout when mirroring methylation data

Issue - State: open - Opened by gsaksena over 7 years ago

#43 - BUG: update gdac_ingestor to reflect latest incarnation of GDCtools

Issue - State: closed - Opened by noblem over 7 years ago - 1 comment

#42 - possible bug in diced_file_comparator

Issue - State: closed - Opened by cbirger over 7 years ago - 2 comments

#41 - Gsaksena methyl

Pull Request - State: closed - Opened by gsaksena over 7 years ago - 4 comments

#40 - dicer does not handle failures appropriately

Issue - State: open - Opened by noblem over 7 years ago

#39 - Cli flags

Pull Request - State: closed - Opened by noblem over 7 years ago

#38 - synonyms and other CLI simplification & rationalization

Issue - State: open - Opened by noblem over 7 years ago - 2 comments

#34 - Updated repo to work with Python3. Included support for direct virtua…

Pull Request - State: closed - Opened by sammeier over 7 years ago - 2 comments

#33 - move tests/diff/bdiff.py to util directory

Issue - State: closed - Opened by noblem over 7 years ago - 1 comment

#32 - calls to requests library should be using session object

Issue - State: open - Opened by noblem over 7 years ago

#31 - Move and update counting

Pull Request - State: closed - Opened by dheiman over 7 years ago

#30 - Minor errors in various files

Pull Request - State: closed - Opened by aswanipranjal over 7 years ago - 6 comments

#29 - How to retrieve data from GDC using Python API

Issue - State: open - Opened by fbrundu over 7 years ago - 3 comments

#28 - Move and update counting

Pull Request - State: closed - Opened by dheiman over 7 years ago - 4 comments

#27 - Move and update counting

Pull Request - State: closed - Opened by dheiman over 7 years ago - 1 comment

#25 - Move heatmap generation to reports

Pull Request - State: closed - Opened by dheiman over 7 years ago

#24 - files/cases needs to be accessible by UUID, too

Issue - State: open - Opened by noblem over 7 years ago

#22 - Add edge case testing for invalid --programs and --project values

Issue - State: closed - Opened by noblem over 7 years ago - 1 comment

#21 - MAF counting is very broken

Issue - State: closed - Opened by noblem over 7 years ago

#20 - draw_heatmaps should be moved from gdc_dice to gdc_report

Issue - State: closed - Opened by noblem over 7 years ago

#19 - sample report should accept title argument at runtime

Issue - State: open - Opened by noblem over 7 years ago

#18 - test_report failure

Issue - State: closed - Opened by noblem over 7 years ago

#17 - gdc_list should not support the full set of CLI flags that gdc_mirror, dice etc do

Issue - State: closed - Opened by noblem over 7 years ago - 1 comment

#16 - Content for WIKI

Issue - State: open - Opened by noblem over 7 years ago

#13 - Helpful error & usage messages for CLI tools

Issue - State: closed - Opened by tmdefreitas almost 8 years ago - 1 comment

#12 - Cannot run tools standalone (i.e. outside of repo directory)

Issue - State: closed - Opened by noblem almost 8 years ago - 2 comments

#11 - tests: we should use vastly smaller subset of data for testing

Issue - State: closed - Opened by noblem about 8 years ago - 1 comment
Labels: enhancement, release_prep

#10 - tests: mirror/dice/report actions are performed but not validated

Issue - State: closed - Opened by noblem about 8 years ago - 3 comments
Labels: enhancement, release_prep

#9 - Nothing mirrored, but dicing still kicked off

Issue - State: closed - Opened by noblem about 8 years ago - 2 comments
Labels: bug, release_prep

#8 - Mirror/Dice version stamp out of sync?

Issue - State: closed - Opened by noblem about 8 years ago
Labels: bug, release_prep

#7 - version stamp used in sample_report: RFE

Issue - State: closed - Opened by noblem about 8 years ago

#6 - non-existent config file should throw error

Issue - State: closed - Opened by noblem about 8 years ago

#5 - tests make it clear that we need a --cases option to select subset of available cases

Issue - State: closed - Opened by noblem about 8 years ago - 1 comment
Labels: enhancement, release_prep

#4 - logging should go into GDCtool base class

Issue - State: closed - Opened by noblem about 8 years ago - 2 comments
Labels: release_prep

#3 - create_loadfile and matplotlib dependency

Issue - State: closed - Opened by noblem about 8 years ago - 1 comment
Labels: bug

#2 - Bad --programs and --projects options should fail immediately

Issue - State: closed - Opened by noblem over 8 years ago - 2 comments