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Use docker container for rules that use R #129

Merged
merged 17 commits into from
May 29, 2024
Merged

Use docker container for rules that use R #129

merged 17 commits into from
May 29, 2024

Commits on Apr 12, 2024

  1. fix: create docker for deseq

    @kelly-sovacool
    kelly-sovacool committed Apr 12, 2024
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  2. fix: use deseq container

    @kelly-sovacool
    kelly-sovacool committed Apr 12, 2024
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Commits on Apr 17, 2024

  1. fix: biocmanager is on cran

    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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  2. fix: use one container for all R scripts & R Markdowns 

    deprecates the Rlib_dir and Rpkg_config parameters and installation code
    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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  3. chore: use mamba install instead of mamba env install 

    because mamba env install just uses conda

related to https://www.github.com/mamba-org/mamba/issues/633
    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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  4. chore: temporarily remove elbow to solve pkg conflicts

    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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  5. fix: install ELBOW manually

    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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  6. chore: fix wget command in docker

    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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  7. docs: update changelog for 129

    @kelly-sovacool
    kelly-sovacool committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. chore: Merge branch 'main' into deseq-docker

    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  2. fix: load the tidyverse

    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  3. fix: correct and simplify singularity args

    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  4. fix: need xfun >= 0.43 in deseq rule

    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  5. refactor: explicitly set scriptsdir param to default in configfile

    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  6. fix: use container for deseq rule 

    accidentally got switched back to envmodule during a merge
    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  7. fix: scripts path for pipeline home

    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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  8. ci: don't run docker auto on PRs 

    save precious GHA runtime
    @kelly-sovacool
    kelly-sovacool committed Apr 18, 2024
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