populationgenomics/analysis-runner issues and pull requests

#688 - Modify HT copy behaviour

Pull Request - State: closed - Opened by MattWellie about 1 month ago

#687 - Upgrade pinned version of cpg-utils in analysis-runner web

Pull Request - State: closed - Opened by dancoates about 1 month ago - 2 comments

#686 - Validation of analysis-runner invocation args

Issue - State: open - Opened by MattWellie about 2 months ago

#685 - Environment Lock

Pull Request - State: closed - Opened by nevoodoo 3 months ago

#684 - Update pinned cpg-utils version in dataproc install common script

Pull Request - State: closed - Opened by EddieLF 3 months ago

#683 - Fix metamist keys for ar-integration

Pull Request - State: closed - Opened by illusional 3 months ago

#682 - Alter Docker build file

Pull Request - State: closed - Opened by MattWellie 3 months ago - 3 comments

#681 - Stream as bytes, not text

Pull Request - State: closed - Opened by illusional 3 months ago

#680 - Quote curl params

Pull Request - State: closed - Opened by illusional 3 months ago

#679 - Update driver image to 1.5

Pull Request - State: closed - Opened by illusional 3 months ago

#678 - Move some methods to cpg-utils

Pull Request - State: closed - Opened by illusional 4 months ago

#677 - Update analysis-runner -> metamist creator script

Pull Request - State: closed - Opened by illusional 4 months ago

#676 - Untar files update

Pull Request - State: open - Opened by EddieLF 4 months ago - 1 comment

#675 - Update linters again

Pull Request - State: closed - Opened by illusional 4 months ago

#674 - Update linters

Pull Request - State: closed - Opened by illusional 4 months ago

#673 - Add branch name as attribute

Pull Request - State: closed - Opened by illusional 4 months ago

#672 - Improve docs + error message

Pull Request - State: closed - Opened by illusional 5 months ago

#671 - Add --storage as CLI argument

Pull Request - State: closed - Opened by MattWellie 6 months ago

#670 - Fix print-identity-token on deploy

Pull Request - State: closed - Opened by illusional 6 months ago

#669 - Revert Dockerfile CMD notation change

Pull Request - State: closed - Opened by illusional 6 months ago

#668 - Unset server-secret during deploy

Pull Request - State: closed - Opened by illusional 6 months ago

#668 - Unset server-secret during deploy

Pull Request - State: closed - Opened by illusional 6 months ago

#667 - Bump + pin web versions

Pull Request - State: closed - Opened by illusional 6 months ago

#667 - Bump + pin web versions

Pull Request - State: closed - Opened by illusional 6 months ago

#666 - Update untar script with cpg_utils import changes

Pull Request - State: closed - Opened by EddieLF 6 months ago

#666 - Update untar script with cpg_utils import changes

Pull Request - State: closed - Opened by EddieLF 6 months ago

#665 - Update README with link to infrastructure-private tokens

Pull Request - State: open - Opened by EddieLF 6 months ago

#665 - Update README with link to infrastructure-private tokens

Pull Request - State: closed - Opened by EddieLF 6 months ago

#664 - Analysis-runner should use latest set of pre-commit hooks

Issue - State: open - Opened by illusional 6 months ago
Labels: good first issue

#664 - Analysis-runner should use latest set of pre-commit hooks

Issue - State: open - Opened by illusional 6 months ago
Labels: good first issue

#663 - Dataproc: Force reinstall of cpg-utils

Pull Request - State: closed - Opened by illusional 6 months ago

#662 - Link to driver job, instead of just batch

Pull Request - State: closed - Opened by illusional 6 months ago - 1 comment

#661 - Analysis runner should convert an floating image tag to a docker digest

Issue - State: open - Opened by illusional 6 months ago

#660 - Extend minimum watch interval

Pull Request - State: closed - Opened by MattWellie 7 months ago - 1 comment

#659 - Fix metadata URL construction + typing

Pull Request - State: closed - Opened by illusional 7 months ago

#658 - Reduce cromwell polling

Pull Request - State: closed - Opened by MattWellie 7 months ago

#657 - Use driver image as default in https transfer jobs

Pull Request - State: closed - Opened by EddieLF 7 months ago

#656 - Use workload identity federation

Pull Request - State: closed - Opened by illusional 7 months ago

#655 - Fix init script path for dataproc

Pull Request - State: closed - Opened by illusional 7 months ago

#654 - Transition examples to use cpg_utils.get_batch

Pull Request - State: closed - Opened by illusional 8 months ago

#653 - Fix tag ordering during deploy

Pull Request - State: closed - Opened by illusional 8 months ago

#652 - Mount secret value directly

Pull Request - State: closed - Opened by illusional 8 months ago

#651 - Ensure ar-guid starts alpha

Pull Request - State: closed - Opened by illusional 8 months ago

#650 - Create copy_gencode_to_main.sh

Pull Request - State: closed - Opened by hopedisastro 9 months ago - 1 comment

#649 - Complete prefix for allowed images in main

Pull Request - State: closed - Opened by MattWellie 9 months ago

#648 - Add ar_guid support to analysis-runner + package

Pull Request - State: closed - Opened by illusional 9 months ago

#647 - Update analysis-server requirements

Pull Request - State: closed - Opened by illusional 9 months ago

#646 - Corrected driver image detection

Pull Request - State: closed - Opened by MattWellie 11 months ago

#645 - Analysis runner bug - assuming config on import

Issue - State: open - Opened by illusional 11 months ago

#644 - Update hail in dataproc and support multiple versions

Pull Request - State: closed - Opened by daniaki 11 months ago

#643 - Pass workflow ID file as a string

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

#642 - Use the existing command wrapper

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

#641 - Import constant within packaged Watcher job

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

#640 - Fixed syntax in job command executing python script

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

#639 - Change to mounted storage directory in unzip wrapper script

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

#638 - Export logs to analysis

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

#637 - Copy out Final Cromwell workflow Logs to a readable directory

Issue - State: open - Opened by MattWellie about 1 year ago

#636 - Bump version: 2.40.8 → 2.40.9

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

#635 - Create copy_cram_for_str.sh

Pull Request - State: open - Opened by hopedisastro about 1 year ago

#634 - Add metamist to driver image

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

#633 - Add script for copying reference truth

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

#632 - correction to cromwell metadata API call

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

#631 - Collected minor fixes

Pull Request - State: closed - Opened by jmarshall about 1 year ago

#630 - Generic files to release

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

#629 - added billing project argument to cram releaser script

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

#628 - Dataproc wheel issue

Issue - State: closed - Opened by illusional about 1 year ago - 1 comment

#627 - update to allow .tar files to be unzipped

Pull Request - State: closed - Opened by EddieLF about 1 year ago - 3 comments

#626 - Create copy_eh_to_analysis.sh

Pull Request - State: closed - Opened by hopedisastro about 1 year ago

#625 - Don't use deprecated download_as_string method

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

#624 - Switch to chunked response encoding

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

#623 - Create copy_female_calls.sh

Pull Request - State: closed - Opened by hopedisastro about 1 year ago

#622 - Create copy_mergedstr.sh

Pull Request - State: closed - Opened by hopedisastro about 1 year ago

#621 - Patch asyncio early

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

#620 - Revert "Limit analysis-runner server workers to 1"

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

#619 - argument to remove filtered rows

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

#618 - Limit analysis-runner server workers to 1

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

#617 - Revert to Hail 0.2.105 for Dataproc once more

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

#616 - Install botocore manually in Dataproc init script

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

#615 - suppress infinite loop failure mode

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

#614 - Cromwell status watcher fix

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

#613 - Remove crams + indexes and somaliers from bucket directory

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

#612 - Try Hail 0.2.110 for Dataproc again

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

#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

GitHub / populationgenomics/analysis-runner issues and pull requests