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Update docker for new viz rules #1

Merged
merged 27 commits into from
May 30, 2024
Merged

Update docker for new viz rules #1

merged 27 commits into from
May 30, 2024

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented May 29, 2024 •
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Changes

  • Merges the latest changes from origin/main, with a slight tweak to the changelog.
  • Adds dependencies to the carlisle_r container and updates it to v2.
  • Uses this container for the new visulation rules introduced in this branch.

Issues

Once this is merged, it will be part of CCBR#132

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • [ ] Update docs if there are any API changes.
  • [ ] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

kelly-sovacool and others added 25 commits April 12, 2024 10:33
@kelly-sovacool
fix: create docker for deseq
e7750ab
@kelly-sovacool
fix: use deseq container
3a51354
@kelly-sovacool
fix: biocmanager is on cran
1d69353
@kelly-sovacool
fix: use one container for all R scripts & R Markdowns
a63ce3f 
deprecates the Rlib_dir and Rpkg_config parameters and installation code
@kelly-sovacool
chore: use mamba install instead of mamba env install
2255b88 
because mamba env install just uses conda

related to https://www.github.com/mamba-org/mamba/issues/633
@kelly-sovacool
chore: temporarily remove elbow to solve pkg conflicts
7ff6150
@kelly-sovacool
fix: install ELBOW manually
f093244
@kelly-sovacool
chore: fix wget command in docker
3593322
@kelly-sovacool
docs: update changelog for 129
10c3fcd
@kelly-sovacool
chore: Merge branch 'main' into deseq-docker
7820ee1
@kelly-sovacool
fix: load the tidyverse
c47737e
@kelly-sovacool
fix: correct and simplify singularity args
f045d50
@kelly-sovacool
fix: need xfun >= 0.43 in deseq rule
8c16205
@kelly-sovacool
refactor: explicitly set scriptsdir param to default in configfile
3d44d1a
@kelly-sovacool
fix: use container for deseq rule
3cba50d 
accidentally got switched back to envmodule during a merge
@kelly-sovacool
fix: scripts path for pipeline home
e784efe
@kelly-sovacool
ci: don't run docker auto on PRs
220d9ea 
save precious GHA runtime
@kelly-sovacool
feat: add parameter to make go_enrichment optional
b99882b
@kelly-sovacool
Merge pull request #129 from CCBR/deseq-docker
4e2b72c 
Use docker container for rules that use R
@kelly-sovacool
docs: update changelog
3ad6798
@kelly-sovacool
feat: make the rose rule optional
8d9a3be 
by request of @epehrsson

related to #134
@kelly-sovacool
Merge branch 'main' into corr-docker
06cf017
@kelly-sovacool
refactor: use docker container for new R rules
23ef8ce
@kelly-sovacool
fix: ComplexHeatmap is on bioc, not cran
29a79d5
@kelly-sovacool
ci: use mamba env create
2a635f3
@kelly-sovacool kelly-sovacool marked this pull request as ready for review May 29, 2024 19:39
@kelly-sovacool kelly-sovacool mentioned this pull request May 29, 2024
Merged
3 tasks
@epehrsson epehrsson merged commit 7b4e33e into CCRGeneticsBranch:correlation May 30, 2024
@kelly-sovacool kelly-sovacool deleted the corr-docker branch May 30, 2024 12:45
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2 participants
@kelly-sovacool @epehrsson