populationgenomics/analysis-runner issues and pull requests

#611 - Hail Batch reads input, set concurrency cap

Pull Request - State: closed - Opened by MattWellie over 1 year ago - 3 comments

#610 - Azure-compatibility

Pull Request - State: open - Opened by violetbrina over 1 year ago

#609 - Revert dataproc image

Pull Request - State: closed - Opened by illusional over 1 year ago

#608 - New dataproc hail version

Pull Request - State: closed - Opened by illusional over 1 year ago

#607 - Release analysis-runner

Pull Request - State: closed - Opened by illusional over 1 year ago

#606 - Use Python3 for private repo token fetching

Pull Request - State: closed - Opened by illusional over 1 year ago

#605 - recursively iterate through extracted paths

Pull Request - State: closed - Opened by EddieLF over 1 year ago - 1 comment

#604 - shuffle original script with a wrapper

Pull Request - State: closed - Opened by MattWellie over 1 year ago - 1 comment

#603 - Download tarball, extract files, upload files, delete files, delete tarball. Simple as.

Pull Request - State: closed - Opened by EddieLF over 1 year ago - 1 comment

#602 - Private repo checkout

Pull Request - State: closed - Opened by illusional over 1 year ago

#601 - Untar to disk

Pull Request - State: closed - Opened by EddieLF over 1 year ago

#600 - hotfix output dir -> output prefix

Pull Request - State: closed - Opened by EddieLF over 1 year ago

#599 - Untar all tarballs in a gcp bucket/subdirectory

Pull Request - State: closed - Opened by EddieLF over 1 year ago

#598 - Better cloud support for analysis-runner

Issue - State: open - Opened by illusional over 1 year ago

#597 - added filenames option for urls with file names

Pull Request - State: closed - Opened by EddieLF over 1 year ago - 1 comment

#596 - Remove disk_usage code

Pull Request - State: closed - Opened by lgruen over 1 year ago

#595 - update method call and config

Pull Request - State: closed - Opened by MattWellie over 1 year ago - 1 comment

#594 - once workflow finishes, parse cromwell output

Pull Request - State: closed - Opened by MattWellie over 1 year ago - 1 comment

#593 - Update to copy crams into release bucket script

Pull Request - State: closed - Opened by EddieLF over 1 year ago - 2 comments

#592 - update to provide project for requester pays

Pull Request - State: closed - Opened by EddieLF over 1 year ago

#591 - Cram releaser

Pull Request - State: closed - Opened by EddieLF over 1 year ago

#590 - Fix config option, + add traceback to server exceptions

Pull Request - State: closed - Opened by illusional over 1 year ago

#589 - Disk usage visualization: color by "hotness", scale cell size by cost

Pull Request - State: closed - Opened by lgruen over 1 year ago

#588 - Fix disk_usage instructions

Pull Request - State: closed - Opened by lgruen over 1 year ago

#587 - Bump version: 2.38.1 → 2.38.2 (Release config CLI fixes)

Pull Request - State: closed - Opened by illusional over 1 year ago

#586 - Unexpected CRAM 'output' values

Issue - State: closed - Opened by MattWellie over 1 year ago - 3 comments

#585 - Update linters

Pull Request - State: closed - Opened by illusional over 1 year ago

#584 - Remove access_group_cache

Pull Request - State: closed - Opened by illusional over 1 year ago

#583 - Fix web service

Pull Request - State: closed - Opened by illusional over 1 year ago

#582 - Bump cpg-utils version in web service

Pull Request - State: closed - Opened by illusional over 1 year ago

#581 - Update group cache members check

Pull Request - State: closed - Opened by illusional over 1 year ago

#580 - Add new infrastructure toml for general infrastructure outputs

Pull Request - State: closed - Opened by illusional over 1 year ago

#579 - subsetting script update

Pull Request - State: closed - Opened by MattWellie over 1 year ago - 6 comments

#578 - Work around bug in setuptools by using a Python 3.10 base image

Pull Request - State: closed - Opened by lgruen over 1 year ago

#577 - Sync Dataproc init scripts automatically

Pull Request - State: closed - Opened by lgruen over 1 year ago

#576 - Generate CPG config from server

Pull Request - State: closed - Opened by illusional over 1 year ago

#575 - Pin crypto package in dataproc init script

Pull Request - State: closed - Opened by vladsavelyev over 1 year ago

#574 - Allow passing an initialization action timeout for Dataproc cluster creation

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#573 - Use gs://cpg-common-main/hail_dataproc instead of gs://cpg-common-main/references/hail_dataproc

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#572 - Update install_common.sh

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#571 - Use gs://cpg-common-main/references instead of gs://cpg-references

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#570 - Remove environment from hailctl.get_deploy_config

Pull Request - State: closed - Opened by illusional almost 2 years ago

#569 - Fix environment config with missing comma

Pull Request - State: closed - Opened by illusional almost 2 years ago

#568 - Environment hotfix

Pull Request - State: closed - Opened by illusional almost 2 years ago

#567 - Initial environment support for single-stack modified format

Pull Request - State: closed - Opened by illusional almost 2 years ago

#566 - Update analysis-runner type

Pull Request - State: closed - Opened by illusional almost 2 years ago

#565 - Allow driver conf override

Pull Request - State: closed - Opened by MattWellie almost 2 years ago - 1 comment

#564 - Bump version: 2.36.4 → 2.36.5

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#563 - allow driver override in config

Pull Request - State: closed - Opened by MattWellie almost 2 years ago

#562 - DRIVER_IMAGE in conf

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

#561 - Add `cpg-workflows` into driver image

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#560 - Hail 0.2.105 for dataproc

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#559 - Merge storage/images/references templates for the baseline config

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#558 - Revert Dataproc switch from 0.2.102 to 0.2.105.

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#557 - Update Dataproc image to Hail 0.2.105

Pull Request - State: closed - Opened by lgruen almost 2 years ago - 1 comment

#556 - Dataproc helper: escape script arguments

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#555 - Fix default user config in Cromwell

Pull Request - State: closed - Opened by illusional almost 2 years ago

#554 - Fix invalid config (server side)

Pull Request - State: closed - Opened by illusional almost 2 years ago

#553 - Set the `genome_build = 'GRCh38'` config value by default

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#552 - Fix init script for dataproc jobs

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#551 - First commit for adding VEP batch backend script

Pull Request - State: closed - Opened by KatalinaBobowik almost 2 years ago - 1 comment

#550 - Update Dataproc version to 0.2.102

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#549 - Fix dataproc init script

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#548 - Take hail package dependencies into account

Pull Request - State: closed - Opened by lgruen almost 2 years ago - 1 comment

#547 - Install Lapack dev libraries for numpy

Pull Request - State: closed - Opened by lgruen almost 2 years ago - 1 comment

#546 - Add indexes to copy to test script

Pull Request - State: closed - Opened by cassimons almost 2 years ago

#545 - Driver: move installing `hail` from source before `analysis-runner`

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago - 4 comments

#544 - Simplify deps

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#543 - Relax pinned versions to be consistent with the hail package

Pull Request - State: closed - Opened by lgruen almost 2 years ago - 3 comments

#542 - Install r-devtools

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#541 - Add script to copy crams/gvcfs for a family to test

Pull Request - State: closed - Opened by cassimons almost 2 years ago - 1 comment

#540 - Require current cpg-utils version

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#539 - Install the correct BioMart package

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#538 - Fix XML library error and add commonly used R packages

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#537 - Add C compiler to R Docker image

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#536 - Add gcloud SDK binaries to PATH

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#535 - Install recent version of gcloud in driver base image

Pull Request - State: closed - Opened by lgruen almost 2 years ago

#534 - update clinvar copy

Pull Request - State: closed - Opened by MattWellie almost 2 years ago

#533 - script for copying clinvar to CPG reference

Pull Request - State: closed - Opened by MattWellie almost 2 years ago - 1 comment

#486 - Fix missing timeouts in analysis-runner

Issue - State: closed - Opened by lgruen about 2 years ago - 1 comment

#392 - Group cache v2

Pull Request - State: closed - Opened by illusional over 2 years ago - 1 comment
Labels: enhancement

#389 - Group membership v2

Issue - State: closed - Opened by illusional over 2 years ago - 1 comment

#354 - Allow depends_on relationship to work with sample-metadata

Pull Request - State: closed - Opened by illusional over 2 years ago - 1 comment

#335 - Projects that have billing disabled break the access group cache

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

#333 - Setup images repo

Issue - State: closed - Opened by illusional over 2 years ago
Labels: enhancement

#329 - Better support external collaborators (read-only depends_on)

Issue - State: closed - Opened by illusional over 2 years ago - 1 comment
Labels: enhancement

GitHub / populationgenomics/analysis-runner issues and pull requests