Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / populationgenomics/analysis-runner issues and pull requests

#707 - Copy recently added server source files to the server image

Pull Request - State: open - Opened by jmarshall 11 days ago

#706 - Don't add comment printing command if there are no comments to print

Pull Request - State: closed - Opened by jmarshall 12 days ago - 1 comment

#705 - Remove gvcf_info from VCF export scripts

Pull Request - State: open - Opened by MattWellie 12 days ago

#704 - Configure Dependabot

Pull Request - State: open - Opened by nevoodoo 16 days ago

#703 - Pip-Audit

Pull Request - State: open - Opened by nevoodoo 16 days ago

#702 - Add sonarqube to test workflow

Pull Request - State: open - Opened by violetbrina 21 days ago

#701 - Add workflow for deploying dataproc image

Pull Request - State: open - Opened by illusional 2 months ago

#700 - More accumulated dataproc Dockerfile changes (and miscellanea)

Pull Request - State: closed - Opened by jmarshall 2 months ago

#699 - Hail 0.2.132 switched from raw setup.py to module build

Pull Request - State: closed - Opened by jmarshall 2 months ago

#698 - Add environment to copy-dataproc-init-script

Pull Request - State: closed - Opened by illusional 2 months ago

#697 - Update dataproc release docs

Pull Request - State: closed - Opened by illusional 2 months ago

#696 - Refactor cromwell endpoint

Pull Request - State: closed - Opened by illusional 2 months ago

#695 - Support repo-less execution + refactor

Pull Request - State: closed - Opened by illusional 2 months ago

#694 - Support repo-less execution + refactor

Pull Request - State: closed - Opened by illusional 2 months ago

#693 - Question

Issue - State: open - Opened by MattWellie 2 months ago - 1 comment

#692 - Fix recursive call

Pull Request - State: closed - Opened by EddieLF 3 months ago - 1 comment

#691 - Use cromwell API, not file

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

#690 - Parse cromwell workflow metadata script

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

#688 - Modify HT copy behaviour

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

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

Pull Request - State: closed - Opened by dancoates 4 months ago - 2 comments

#686 - Validation of analysis-runner invocation args

Issue - State: open - Opened by MattWellie 5 months ago

#685 - Environment Lock

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

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

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

#683 - Fix metamist keys for ar-integration

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

#682 - Alter Docker build file

Pull Request - State: closed - Opened by MattWellie 6 months ago - 3 comments

#681 - Stream as bytes, not text

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

#680 - Quote curl params

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

#679 - Update driver image to 1.5

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

#678 - Move some methods to cpg-utils

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

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

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

#676 - Untar files update

Pull Request - State: open - Opened by EddieLF 7 months ago - 1 comment

#675 - Update linters again

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

#674 - Update linters

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

#673 - Add branch name as attribute

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

#672 - Improve docs + error message

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

#671 - Add --storage as CLI argument

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

#670 - Fix print-identity-token on deploy

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

#669 - Revert Dockerfile CMD notation change

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

#668 - Unset server-secret during deploy

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

#668 - Unset server-secret during deploy

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

#667 - Bump + pin web versions

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

#667 - Bump + pin web versions

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

#666 - Update untar script with cpg_utils import changes

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

#666 - Update untar script with cpg_utils import changes

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

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

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

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

Pull Request - State: open - Opened by EddieLF 9 months ago

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

Issue - State: open - Opened by illusional 9 months ago
Labels: good first issue

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

Issue - State: open - Opened by illusional 9 months ago
Labels: good first issue

#663 - Dataproc: Force reinstall of cpg-utils

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

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

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

#660 - Extend minimum watch interval

Pull Request - State: closed - Opened by MattWellie 10 months ago - 1 comment

#659 - Fix metadata URL construction + typing

Pull Request - State: closed - Opened by illusional 10 months ago

#658 - Reduce cromwell polling

Pull Request - State: closed - Opened by MattWellie 10 months ago

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

Pull Request - State: closed - Opened by EddieLF 10 months ago

#656 - Use workload identity federation

Pull Request - State: closed - Opened by illusional 10 months ago

#655 - Fix init script path for dataproc

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

#654 - Transition examples to use cpg_utils.get_batch

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

#653 - Fix tag ordering during deploy

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

#652 - Mount secret value directly

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

#651 - Ensure ar-guid starts alpha

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

#650 - Create copy_gencode_to_main.sh

Pull Request - State: closed - Opened by hopedisastro 12 months ago - 1 comment

#649 - Complete prefix for allowed images in main

Pull Request - State: closed - Opened by MattWellie 12 months ago

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

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

#647 - Update analysis-server requirements

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

#646 - Corrected driver image detection

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

#645 - Analysis runner bug - assuming config on import

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

#644 - Update hail in dataproc and support multiple versions

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

#643 - Pass workflow ID file as a string

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

#642 - Use the existing command wrapper

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

#641 - Import constant within packaged Watcher job

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

#640 - Fixed syntax in job command executing python script

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

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

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

#638 - Export logs to analysis

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

#636 - Bump version: 2.40.8 → 2.40.9

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

#635 - Create copy_cram_for_str.sh

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

#634 - Add metamist to driver image

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

#633 - Add script for copying reference truth

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

#632 - correction to cromwell metadata API call

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

#631 - Collected minor fixes

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

#630 - Generic files to release

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

#629 - added billing project argument to cram releaser script

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

#628 - Dataproc wheel issue

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

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

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

#626 - Create copy_eh_to_analysis.sh

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

#625 - Don't use deprecated download_as_string method

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

#624 - Switch to chunked response encoding

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

#623 - Create copy_female_calls.sh

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

#622 - Create copy_mergedstr.sh

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

#621 - Patch asyncio early

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

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

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

#619 - argument to remove filtered rows

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

#618 - Limit analysis-runner server workers to 1

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

#617 - Revert to Hail 0.2.105 for Dataproc once more

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

#616 - Install botocore manually in Dataproc init script

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

#615 - suppress infinite loop failure mode

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

#614 - Cromwell status watcher fix

Pull Request - State: closed - Opened by MattWellie over 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