Code

First draft of GitHub Actions#161

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bio-la merged 23 commits intomainDendrouLab/panpipes:mainfrom kra-ghaDendrouLab/panpipes:kra-ghaCopy head branch name to clipboardFeb 8, 2024

+126

Commits

Commits on Feb 2, 2024

• install miniconda

  kevinrue

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  a1f85cf

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• specify shell bash -l

  kevinrue

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  d590a49

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• add more trigger events

  kevinrue

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• move workflow file in the right place

  kevinrue

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• use conda-incubator/setup-miniconda@v3

  kevinrue

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  d0ef13b

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• install r-base in pipeline environment

  kevinrue

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• checkout repo

  kevinrue

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• install dependencies via yaml file

  kevinrue

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• install dependencies via setup-miniconda

  kevinrue

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• use bash -el for all conda commands

  kevinrue

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• remove duplicate python spec

  kevinrue

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Commits on Feb 5, 2024

• disable tests and prepare data and configuration

  kevinrue

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• bash el to activate environment

  kevinrue

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• rename workflow and jobs

  kevinrue

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• set up config file and submission file

  kevinrue

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  b8f2271

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• do not checkout the repo, download YAML file only

  kevinrue

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  094bd91

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• final setup and run

  kevinrue

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• show file tree at the end of setup

  kevinrue

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  4c775fe

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• fix filenames

  kevinrue

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• cd into the expected place

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• cd in all relevant steps of workflow

  kevinrue

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  a46a822

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• curl -L to follow redirects

  kevinrue

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  d91ee0b

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• fix path of pipeline config

  kevinrue

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