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Start wilms analysis#681

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jaclyn-taroni merged 49 commits intoAlexsLemonade:mainAlexsLemonade/OpenScPCA-analysis:mainfrom maud-p:start-wilms-analysismaud-p/OpenScPCA-analysis:start-wilms-analysisCopy head branch name to clipboardAug 5, 2024

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Commits on Jul 23, 2024

• Create download-data.py

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Commits on Jul 25, 2024

• create module 1

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• Update Dockerfile

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Commits on Jul 29, 2024

• Update README.md

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• Add files via upload

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• Update GeneticAlterations_metadata.csv

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• Update README.md

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Commits on Jul 30, 2024

• changes to issue AlexsLemonade#671

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Commits on Aug 1, 2024

• Update analyses/cell-type-wilms-tumor-06/Dockerfile

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• Update analyses/cell-type-wilms-tumor-06/Dockerfile

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• Update analyses/cell-type-wilms-tumor-06/README.md

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• Update analyses/cell-type-wilms-tumor-06/README.md

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• Update analyses/cell-type-wilms-tumor-06/README.md

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• Update analyses/cell-type-wilms-tumor-06/README.md

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Commits on Aug 2, 2024

• Update Dockerfile

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• change inpu data

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• update_data_download_steps

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• add sample metadata information

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• remove unused mount directories

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• remove unused volumes

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• adding renv.lock file

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Commits on Aug 3, 2024

• Remove lock file (potentially temporarily!)

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• Base image with RStudio that's compatible with ARM + renv

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• Commit output from renv::init()

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• Add an empty dependencies.R file

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• Add tidyverse to dependencies

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• Update lockfile after library(tidyverse)

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• Uncomment renv steps from Dockerfile

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• Snapshot with some single-cell packages

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• renv::update()

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• Stub in run workflow; don't uncomment on PR

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• Add Docker build and push for Wilms cell typing module

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• Add to list of modules with Docker images

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• Document experience with Docker and renv

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Commits on Aug 4, 2024

• Remove files specific to Halbritter lab setup and stop tracking

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• Add newline

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• Merge pull request #3 from jaclyn-taroni/jaclyn-taroni/wilms-06-build-test

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Commits on Aug 5, 2024

• Create run.sh

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• DOI Correction

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• DOI Correction

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• Rename run.sh to run-podman-internal.sh

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• Update run-podman-internal.sh

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• Update analyses/cell-type-wilms-tumor-06/README.md

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• Update README.md halbritter specific section to run container

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• Merge branch 'main' into start-wilms-analysis

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