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add ottr_viz image #15

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bde2359
add ottr_viz image
kweav Feb 3, 2026
d434230
Update Dockerfile to include maintainer email
kweav Feb 27, 2026
4f1bccd
Update Dockerfile with python package for text coloring
kweav Mar 19, 2026
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16 changes: 12 additions & 4 deletions .github/pull_request_template.md
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@@ -1,14 +1,22 @@
<!-- From https://axolo.co/blog/p/part-3-github-pull-request-template-->
<!-- From https://axolo.co/blog/p/part-3-github-pull-request-template-->

# Description

<!-- Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change. -->
<!-- Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change. -->

Fixes # (issue)

## Checklist (if adding a new docker image)

- [ ] image in new directory
- [ ] file in that directory named 'Dockerfile' exactly
- [ ] image has been built or tested / passes tests
- [ ] image added to `pull_request.yml` file (following `- {dir: directory_path, name: 'name its called on dockerhub'}` convention)
- [ ] image added to `merge.yml` file (following `- {dir: directory_path, name: 'name its called on dockerhub'}` convention)

## Type of change

<!-- Please delete options that are not relevant. -->
<!-- Please delete options that are not relevant. -->

- [ ] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
Expand All @@ -17,7 +25,7 @@ Fixes # (issue)

# How Has This Been Tested?

<!-- Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration -->
<!-- Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration -->

- [ ] Test A
- [ ] Test B
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1 change: 1 addition & 0 deletions .github/workflows/merge.yml
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Expand Up @@ -28,6 +28,7 @@ jobs:
- {dir: ottr_itn_workshop, name: 'jhudsl/ottr_itn_workshop'}
- {dir: ottr_metrics, name: 'jhudsl/ottr_metrics'}
- {dir: ottr_ml, name: 'jhudsl/ottr_ml'}
- {dir: ottr_viz, name: 'jhudsl/ottr_viz'}
# NEW IMAGES HERE: #
####### - {dir: directory_path, name: 'name its called on dockerhub'}
steps:
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1 change: 1 addition & 0 deletions .github/workflows/pull_request.yml
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Expand Up @@ -25,6 +25,7 @@ jobs:
- {dir: ottr_itn_workshop, name: 'jhudsl/ottr_itn_workshop'}
- {dir: ottr_metrics, name: 'jhudsl/ottr_metrics'}
- {dir: ottr_ml, name: 'jhudsl/ottr_ml'}
- {dir: ottr_viz, name: 'jhudsl/ottr_viz'}
# NEW IMAGES HERE: #
####### - {dir: directory_path, name: 'name its called on dockerhub'}
steps:
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51 changes: 51 additions & 0 deletions ottr_viz/Dockerfile
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FROM jhudsl/ottr_python:main
LABEL maintainer="kisaac@fredhutch.org"

# Remove broken Vivaldi repo
RUN rm -f /etc/apt/sources.list.d/vivaldi.list \
&& rm -f /etc/apt/sources.list.d/vivaldi*.sources

# System dependencies for R packages
RUN apt-get update && apt-get install -y \
cmake \
xz-utils \
libgmp-dev \
libudunits2-dev \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libfontconfig1-dev \
libfreetype6-dev \
libharfbuzz-dev \
libfribidi-dev \
libpng-dev \
libjpeg-dev \
libtiff-dev \
libcairo2-dev \
libgit2-dev \
&& rm -rf /var/lib/apt/lists/*

# Install BiocManager
RUN Rscript -e "install.packages('BiocManager', repos='https://cloud.r-project.org')"

# Install nloptr early (compiled dependency)
RUN Rscript -e "BiocManager::install('nloptr')"

# Core R infrastructure (pinned versions)
RUN Rscript -e "install.packages( \
c('Rcpp', 'xfun', 'htmltools', 'rmarkdown', 'knitr'), \
repos='https://cloud.r-project.org')"

# Plotting ecosystem (pinned versions)
RUN Rscript -e "install.packages( \
c('ggpubr','patchwork','broom','ggrepel','ggtext','ggrain','ggridges', \
'networkD3','scales','survival','survMisc','survminer','ggVennDiagram', \
'UpSetR','naniar','palmerpenguins'), \
repos='https://cloud.r-project.org')"

# remotes + GitHub packages
RUN Rscript -e "install.packages('remotes', repos='https://cloud.r-project.org')"
RUN Rscript -e "remotes::install_github('davidsjoberg/ggsankey')"

# Python packages
RUN pip3 install adjustText==1.3.0 highlight-text
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