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Start wilms analysis #681

Merged
merged 49 commits into from
Aug 5, 2024
Merged

Start wilms analysis #681

merged 49 commits into from
Aug 5, 2024

Commits on Jul 23, 2024

  1. Create download-data.py

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    maud-p authored Jul 23, 2024
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Commits on Jul 25, 2024

  1. create module 1

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    maud-p committed Jul 25, 2024
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  2. Update Dockerfile

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    maud-p authored Jul 25, 2024
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Commits on Jul 29, 2024

  1. Update README.md

    @maud-p
    maud-p authored Jul 29, 2024
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  2. Update README.md

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    maud-p authored Jul 29, 2024
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  3. Add files via upload

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    maud-p authored Jul 29, 2024
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  4. Update GeneticAlterations_metadata.csv

    @maud-p
    maud-p authored Jul 29, 2024
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  5. Update README.md

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    maud-p authored Jul 29, 2024
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  6. Update README.md

    @maud-p
    maud-p authored Jul 29, 2024
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  7. Update README.md

    @maud-p
    maud-p authored Jul 29, 2024
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  8. Update README.md

    @maud-p
    maud-p authored Jul 29, 2024
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Commits on Jul 30, 2024

  1. changes to issue AlexsLemonade#671

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    maud-p committed Jul 30, 2024
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Commits on Aug 1, 2024

  1. Update analyses/cell-type-wilms-tumor-06/Dockerfile 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 1, 2024
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  2. Update analyses/cell-type-wilms-tumor-06/Dockerfile 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 1, 2024
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  3. Update analyses/cell-type-wilms-tumor-06/README.md 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 1, 2024
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  4. Update analyses/cell-type-wilms-tumor-06/README.md 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 1, 2024
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  5. Update analyses/cell-type-wilms-tumor-06/README.md 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 1, 2024
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  6. Update analyses/cell-type-wilms-tumor-06/README.md 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 1, 2024
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Commits on Aug 2, 2024

  1. Update Dockerfile

    @maud-p
    maud-p authored Aug 2, 2024
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  2. change inpu data

    @maud-p
    maud-p authored Aug 2, 2024
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  3. update_data_download_steps

    @maud-p
    maud-p authored Aug 2, 2024
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  4. add sample metadata information

    @maud-p
    maud-p authored Aug 2, 2024
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  5. remove unused mount directories

    @maud-p
    maud-p authored Aug 2, 2024
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  6. remove unused volumes

    @maud-p
    maud-p authored Aug 2, 2024
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  7. adding renv.lock file

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    maud-p authored Aug 2, 2024
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Commits on Aug 3, 2024

  1. Remove lock file (potentially temporarily!)

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  2. Base image with RStudio that's compatible with ARM + renv

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  3. Commit output from renv::init()

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    jaclyn-taroni committed Aug 3, 2024
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  4. Add an empty dependencies.R file

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  5. Add tidyverse to dependencies

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  6. Update lockfile after library(tidyverse)

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    jaclyn-taroni committed Aug 3, 2024
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  7. Uncomment renv steps from Dockerfile

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  8. Snapshot with some single-cell packages

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  9. renv::update()

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    jaclyn-taroni committed Aug 3, 2024
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  10. Stub in run workflow; don't uncomment on PR

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    jaclyn-taroni committed Aug 3, 2024
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  11. Add Docker build and push for Wilms cell typing module

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  12. Add to list of modules with Docker images

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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  13. Document experience with Docker and renv

    @jaclyn-taroni
    jaclyn-taroni committed Aug 3, 2024
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Commits on Aug 4, 2024

  1. Remove files specific to Halbritter lab setup and stop tracking

    @jaclyn-taroni
    jaclyn-taroni committed Aug 4, 2024
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  2. Add newline

    @jaclyn-taroni
    jaclyn-taroni committed Aug 4, 2024
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  3. Merge pull request #3 from jaclyn-taroni/jaclyn-taroni/wilms-06-build… 

    …-test

Build and test Docker image using `bioconductor/bioconductor_docker:3.19` and `renv`
    @maud-p
    maud-p authored Aug 4, 2024
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Commits on Aug 5, 2024

  1. Create run.sh

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    maud-p authored Aug 5, 2024
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  2. DOI Correction

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    maud-p authored Aug 5, 2024
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  3. DOI Correction

    @maud-p
    maud-p authored Aug 5, 2024
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  4. Rename run.sh to run-podman-internal.sh

    @maud-p
    maud-p authored Aug 5, 2024
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  5. Update run-podman-internal.sh

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    maud-p authored Aug 5, 2024
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  6. Update analyses/cell-type-wilms-tumor-06/README.md 

    Co-authored-by: Jaclyn Taroni <[email protected]>
    @maud-p @jaclyn-taroni
    maud-p and jaclyn-taroni authored Aug 5, 2024
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  7. Update README.md halbritter specific section to run container

    @maud-p
    maud-p authored Aug 5, 2024
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  8. Merge branch 'main' into start-wilms-analysis

    @jaclyn-taroni
    jaclyn-taroni authored Aug 5, 2024
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