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Anvil update #474

Closed
wants to merge 64 commits into from
Closed

Anvil update #474

wants to merge 64 commits into from

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ksuderman
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Merge changes from the main branch.

almahmoud and others added 30 commits August 13, 2021 19:16
@almahmoud
Changes for not mounting entire NFS to each job
4e27f15 
friends with galaxyproject/galaxy#12345
@almahmoud
Separate data and working dir pvcs
bb53d37
@nuwang
Removed unnecessary mounts and made inputs read only
380430d
@ksuderman
Remove spaces that makes helm lint unhappy
4138130
@ksuderman
First pass at defining cron jobs in the values.yaml file.
e0b960d
@ksuderman
Fix command formatting and quoting
9c84d17
@ksuderman
Remove nodeSelector
d2941d7
@ksuderman
Tmp cleanup and maintenance scripts are treated as special cases.
95474e2
@ksuderman
Update the name of the container used to run the maintenance script.
93930d7
@ksuderman
Define all cron jobs in the values.yaml file again, but allows time d…
287cf13 
…urations to be parameterized.
@nuwang
Use walltime limit for cleanup and other minor tweaks
8225be5
@nuwang
Change find units from seconds to days
8cc5d94
@ksuderman
Parameterize the nodeSelector
64320c8
@ksuderman
Remove the chown cron job
2bbaa3a
@ksuderman
Reverting my revert
df1fb39
@ksuderman
Add extraFileMappings for cron jobs
247cbf5
@ksuderman
Start documenting cron jobs
cf77963
@ksuderman
Make the galaxy.yml file available in a configmap for the maintenance…
13e4f0b 
… cronjob
@ksuderman @nuwang
Update galaxy/values.yaml
27fd304 
Co-authored-by: Nuwan Goonasekera <[email protected]>
@ksuderman
Add helper to calculate the postgres connection string
42488ff
@ksuderman
Add cron job documentation and remove Galaxy versions section
0fafea8
@ksuderman
Add env definitions
497b572
@ksuderman
Maintenace job should include default env vars
da6a97a
@ksuderman @nuwang
Update galaxy/values.yaml
cdc2a98 
Co-authored-by: Nuwan Goonasekera <[email protected]>
@ksuderman @nuwang
Update galaxy/values.yaml
63bc997 
Co-authored-by: Nuwan Goonasekera <[email protected]>
@ksuderman
Parameterize Docker image for cron jobs
d96979a
@ksuderman
Allow mode (permissions) to be defined on extraFileMappings
3af24cd
@ksuderman
Add YAML document separators (triple dashes) to the start of yaml tem…
b058b5e 
…plates.
@ksuderman
Add example cron job
3fe5723
@ksuderman
Additional documentation for cron jobs
07fdbd4
ksuderman and others added 25 commits April 17, 2024 12:06
@ksuderman
Update all checkout actions to v4
576807e
@nuwang
Merge pull request galaxyproject#463 from ksuderman/482-release-notes
8b4631d 
Fix release notes generation
@nuwang
Merge pull request galaxyproject#458 from ksuderman/document-separators
9f45b8c 
Add YAML document separators
@actions-user
Automatic Version Bumping from 5.10.0 to 5.10.1
60a4ecc
@nuwang
Merge pull request galaxyproject#460 from galaxyproject/encouraging-s…
050af87 
…callop

Run tests with 1.28, and add missing tool versions to sanitize allowlist
@actions-user
Automatic Version Bumping from 5.10.1 to 5.11.0
ba6afdd
@ksuderman
Set user.name and user.email for the GitHub bot
9df267e
@ksuderman
Merge branch 'master' into 408-maintenance
a7c1aed
@ksuderman
Add newline to the end of the file.
14f190d
@nuwang
Merge pull request galaxyproject#466 from ksuderman/465-bot-email
87cfd68 
Set committer info for the GitHub bot
@nuwang
Merge pull request galaxyproject#448 from ksuderman/408-maintenance
72f95ad 
Cron job maintenance
@actions-user
Automatic Version Bumping from 5.11.0 to 5.12.0
2e32eac
@ksuderman
Add enabled flag to the actions
7e61ac1
@ksuderman @nuwang
Update galaxy/templates/cronjob-maintenance.yaml
bbdbdb9 
Co-authored-by: Nuwan Goonasekera <[email protected]>
@nuwang
Merge pull request galaxyproject#468 from ksuderman/408-maintenance-e…
eedf472 
…nable

Add enable flag to cron jobs
@nuwang @ksuderman
Update README.md
68be5df
@ksuderman
Document enabled flag for cron jobs
17e8292
@ksuderman
Persist credentials and set GH_TOKEN for the GitHub command line tool
7fe918b
@nuwang
Merge pull request galaxyproject#470 from ksuderman/462-release-notes
38f62a8 
Persist credentials and set GH_TOKEN for the GitHub command line tool
@actions-user
Automatic Version Bumping from 5.12.0 to 5.12.1
c16ea12
@nuwang
Merge pull request galaxyproject#469 from ksuderman/408-readme
2c3aeaf 
Document enabled flag for cron jobs
@actions-user
Automatic Version Bumping from 5.12.1 to 5.13.0
d918841
@ksuderman
Ensure tag-and-release checks out the latest commits make by the helm…
431c683 
…-ci action.
@nuwang
Merge pull request galaxyproject#473 from ksuderman/472-checkout-latest
fdc086f 
Checkout latest commit made by helm-ci action
@ksuderman
Updating AnVIL branch to latest Galaxy Helm
4f7ef31
@ksuderman ksuderman requested review from afgane and nuwang May 7, 2024 19:37
afgane
afgane reviewed May 8, 2024
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@afgane afgane left a comment

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This all looks good but we should not merge until our CVMFS-CSI chart is synced with the latest upstream version and that update propagated to this chart.

@afgane
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afgane commented May 8, 2024

Here's a PR updating the CVMFS-CSI (& Galaxy): #475

@nuwang nuwang closed this Sep 10, 2024
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@afgane afgane afgane left review comments

@nuwang nuwang Awaiting requested review from nuwang

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5 participants
@ksuderman @afgane @nuwang @almahmoud @actions-user