Arvados

Story

Resolved

Rejected

Sprint Impediments

9037

[Microsoft] [bcbio] Rewrite CWL workflows to take advantage of Arvados provenance

Jiayong Li

303

impediments

-c-a

9040

[BD] Clean up Genevia pipeline for useability

Bryan Cosca

189

impediments

-c-a

9060

[bcbio] Automatically generate CWL workflows that take advantage of Arvados provenance

Brad Chapman

188

impediments

-c-a

9069

[BDT] Migrate pipeline to RDS

Brett Smith

impediments

-c-a

9071

[OPS] Set up a new cluster for Microsoft

Nico César

288

impediments

-c-a

9073

[Microsoft] [bcbio] Enable bcbio generation of CWL to flag gVCF output for Freebayes

Brad Chapman

188

impediments

-c-a

9074

[Microsoft] [bcbio] Enable bcbio generation of CWL to flag gVCF output for GATK Haplotypecaller

Brad Chapman

188

impediments

-c-a

9113

[Microsoft] [bcbio] Enable bcbio generation of CWL to flag gVCF output for Platypus

Brad Chapman

188

impediments

-c-a

8087 8087 Joshua Randall Joshua Randall 196 SDKs 54 SDKs [SDKs] `arv create` can read JSON from a file, skipping an interactive editor Resolved Resolved 3 0.5 0.5 0.5 8087 36 196 136 6 0.5	8519 8519 Review PR #43 Joshua Randall 196 0 8087 3 36 -c-a 5
8876 8876 Radhika Chippada Radhika Chippada 72 [Workbench] Unify job and pipeline instance show tabs using Work Unit interface Resolved Resolved 3 2.0 2.0 2.0 8876 36 72 136 6 2.0	9207 9207 Review branch 8876-work-unit Tom Clegg 3 0 8876 3 36 -c-a 5
9275 9275 Radhika Chippada Radhika Chippada 72 [CWL] arvados-cwl-runner creates job components instead of pipeline instance Resolved Resolved 3 1.0 1.0 1.0 9275 36 72 136 2 1.0	9295 9295 Review branch 9275-cwl-runner-creates-jobs Peter Amstutz 47 0 9275 3 36 -c-a 5
9187 9187 Peter Amstutz Peter Amstutz 47 Crunch 52 Crunch [Crunch2] Update dispatcher to use new API support Resolved Resolved 3 1.0 1.0 1.0 9187 36 47 136 6 1.0	9196 9196 Review 9187-crunchv2-dispatching Tom Clegg 3 0 9187 3 36 -c-a 5 9195 9195 Update local dispatcher Peter Amstutz 47 0 9187 3 36 -c-a 5 9194 9194 Update slurm dispatcher Peter Amstutz 47 0 9187 3 36 -c-a 5 9365 9365 Review 9187-requeued-containers Tom Clegg 3 0 9187 3 36 -c-a 5
9343 9343 Tom Clegg Tom Clegg 3 Keep 53 Keep [Keep] MakeArvadosClient is asking for extra unneded environment variables Resolved Resolved 3 0.5 0.5 0.5 9343 36 3 136 1 0.5
8905 8905 Brett Smith Brett Smith 79 [Deployment] arvados-sso-server deb package unnecessarily depends on "postgresql" meta-package Resolved Resolved 3 0.5 0.5 0.5 8905 36 79 136 1 0.5
9272 9272 Tom Clegg Tom Clegg 3 [Crunch2] Pass container auth token (not dispatch token) to arv-mount, and (if requested) into the container itself Resolved Resolved 3 1.0 1.0 1.0 9272 36 3 136 2 1.0	9299 9299 Retrieve & use correct token Tom Clegg 3 0 9272 3 36 -c-a 5 9291 9291 Review 9272-use-container-auth Tom Clegg 3 0 9272 3 36 -c-a 5 9305 9305 Review 9272-test-races Peter Amstutz 47 0 9272 3 36 -c-a 5 9306 9306 (extras) fix state transitions to match API rules Tom Clegg 3 0 9272 3 36 -c-a 5
9233 9233 Bryan Cosca Bryan Cosca 189 Fix Ancestry Mapper pipeline Resolved Resolved 3 0.5 0.5 0.5 9233 36 189 136 1 0.5
9162 9162 Tom Clegg Tom Clegg 3 [Block Manager] Trashes unreferenced blocks (with mtime > TTL if desired) and overreplicated block Resolved Resolved 3 0.5 0.5 0.5 9162 36 3 136 6 0.5	9206 9206 Build data-block map Tom Clegg 3 0 9162 3 36 -c-a 5 9209 9209 Recommend trash/pull operations for a block Tom Clegg 3 0 9162 3 36 -c-a 5 9210 9210 Buffer trash/pull operations and forward to keepstores Tom Clegg 3 0 9162 3 36 -c-a 5 9235 9235 Accept keep services list in config Tom Clegg 3 0 9162 3 36 -c-a 5 9237 9237 run as a service, wake up on timer and SIGUSR1 Tom Clegg 3 0 9162 3 36 -c-a 5 9229 9229 docs and lint Tom Clegg 3 0 9162 3 36 -c-a 5 9300 9300 Build & publish package Tom Clegg 3 0 9162 3 36 -c-a 5 9211 9211 Review 9162-keep-balance Radhika Chippada 72 0 9162 3 36 -c-a 5
9242 9242 Brett Smith Brett Smith 79 Deployment 60 Deployment [Deployment] python-six backport breaks other users Resolved Resolved 3 9242 36 79 136 1	9247 9247 Review 9242-python-backport-prefix-wip Ward Vandewege 1 0 9242 3 36 -c-a 5
9316 9316 Brett Smith Brett Smith 79 [SDKs] CWL SDK package needs to include its own README.rst Resolved Resolved 3 9316 36 79 136 1