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Add snakemake plugin to webservice image #6097

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Merged
denis-yuen merged 4 commits into from
Apr 15, 2025
Merged

Add snakemake plugin to webservice image #6097

denis-yuen merged 4 commits into from
Apr 15, 2025

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@denis-yuen
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@denis-yuen denis-yuen commented Apr 11, 2025 •
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Description
Add snakemake plugin to webservice image

Review Instructions
Can download and look for Snakemake plugin in Docker image, should also have an additional message in qa web logs

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-7016

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Please make sure that you've checked the following before submitting your pull request. Thanks!

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@denis-yuen denis-yuen self-assigned this Apr 11, 2025
@denis-yuen denis-yuen changed the title WIP, needs testing but artifactory down Add snakemake plugin to webservice image Apr 14, 2025
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codecov bot commented Apr 14, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.24%. Comparing base (3f6e5c7) to head (3ade936).
Report is 1 commits behind head on develop.

Additional details and impacted files 
@@            Coverage Diff             @@
##             develop    #6097   +/-   ##
==========================================
  Coverage      74.24%   74.24%           
  Complexity      5663     5663           
==========================================
  Files            389      389           
  Lines          20343    20343           
  Branches        2103     2103           
==========================================
  Hits           15104    15104           
  Misses          4237     4237           
  Partials        1002     1002
Flag Coverage Δ
bitbuckettests 26.02% <ø> (ø)
hoverflytests 27.66% <ø> (ø)
integrationtests 56.06% <ø> (ø)
languageparsingtests 10.81% <ø> (ø)
localstacktests 21.32% <ø> (ø)
toolintegrationtests 29.88% <ø> (ø)
unit-tests_and_non-confidential-tests 26.27% <ø> (ø)
workflowintegrationtests 37.50% <ø> (ø)

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@denis-yuen denis-yuen marked this pull request as ready for review April 14, 2025 17:50
@denis-yuen denis-yuen requested review from a team, hyunnaye, kathy-t and svonworl and removed request for a team April 14, 2025 17:51
kathy-t
kathy-t approved these changes Apr 15, 2025
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# Include snakemake language plugin
ARG snakemake_plugin_version=0.0.3
RUN apt-get install -y wget
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@kathy-t kathy-t Apr 15, 2025

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Isn't wget already installed on line 22?

Similarly, the language-plugins directory is also created on line 23

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@svonworl svonworl Apr 15, 2025

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We could move the apt-get and mkdir into separate "prepare to get plugins" block, above the galaxy download, to make it more clear and so that the galaxy download block and snakemake download block both look the same.

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sonarqubecloud bot commented Apr 15, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@denis-yuen denis-yuen merged commit 8094a60 into develop Apr 15, 2025
23 checks passed
@denis-yuen denis-yuen deleted the feature/add_plugin_smk branch April 15, 2025 20:11
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@svonworl svonworl svonworl approved these changes

@hyunnaye hyunnaye Awaiting requested review from hyunnaye hyunnaye was automatically assigned from dockstore/dockstore

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@kathy-t kathy-t kathy-t approved these changes

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