diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
new file mode 100644
index 0000000..a437049
--- /dev/null
+++ b/.github/workflows/check-url.yml
@@ -0,0 +1,107 @@
+name: Periodic URL Check
+
+on:
+ workflow_dispatch:
+ schedule:
+ - cron: '0 0 1 * *'
+
+jobs:
+ set-up:
+ name: Load user automation choices
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+
+ # Use the yaml-env-action action.
+ - name: Load environment from YAML
+ uses: doughepi/yaml-env-action@v1.0.0
+ with:
+ files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+ outputs:
+ toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
+
+ url-check:
+ name: Check URLs
+ needs: set-up
+ if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
+ runs-on: ubuntu-latest
+ container:
+ image: jhudsl/base_ottr:main
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+
+ # Delete the branch if this has been run before
+ - name: Delete branch locally and remotely
+ run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+ # Make the branch fresh
+ - name: Make the branch fresh
+ run: |
+ git config --global --add safe.directory $GITHUB_WORKSPACE
+ git config --global user.name 'github-actions[bot]'
+ git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+ echo branch doesnt exist
+ git checkout -b preview-spell-error || echo branch exists
+ git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+ shell: bash
+
+ - name: Run the check
+ uses: jhudsl/ottr-reports@main
+ id: check_results
+ continue-on-error: true
+ with:
+ check_type: urls
+ error_min: 1
+
+ - name: Declare file path and time
+ id: check-report
+ run: |
+ error_num=$(cat check_reports/url_checks.tsv | wc -l)
+ error_num="$((error_num-1))"
+ echo "error_num=$error_num" >> $GITHUB_OUTPUT
+ echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
+ shell: bash
+
+ - name: Stop if failure
+ if: steps.check_results.outcome == 'failure'
+ run: exit 1
+
+ - name: Print out error variables
+ run: |
+ echo ${{ steps.check-report.outputs.error_url }}
+ echo ${{ steps.check-report.outputs.error_num }}
+
+ - name: Find issues
+ id: find-issue
+ env:
+ GH_PAT: ${{ secrets.GH_PAT }}
+ run: |
+ echo "$GITHUB_REPOSITORY"
+ curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R
+ issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
+ echo URL issue exists: $issue_exists
+ echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
+
+ - name: If too many URL errors, then make an issue
+ if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
+ uses: JasonEtco/create-an-issue@v2
+ with:
+ filename: .github/ISSUE_TEMPLATE/url-error.md
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ FILE_URL: ${{ steps.check-report.outputs.error_url }}
+ ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+ - name: If no URL errors than delete the branch we made
+ if: ${{ steps.check-report.outputs.error_num < 1 }}
+ run: |
+ git config --system --add safe.directory "$GITHUB_WORKSPACE"
+ git push origin --delete preview-spell-error || echo "No branch to delete"
diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
index afd658a..faa83cc 100644
--- a/.github/workflows/delete-preview.yml
+++ b/.github/workflows/delete-preview.yml
@@ -18,7 +18,7 @@ jobs:
# Check out current repository
- name: checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
deleted file mode 100644
index 77491cb..0000000
--- a/.github/workflows/docker-build.yml
+++ /dev/null
@@ -1,79 +0,0 @@
-# Candace Savonen Apr 2021
-
-name: Build Docker
-
-on:
- workflow_dispatch:
- inputs:
- dockerhubpush:
- description: 'Push to Dockerhub?'
- required: true
- default: 'false'
- tag:
- description: 'What tag to use?'
- required: true
- default: 'none'
-jobs:
- build-docker:
- name: Build Docker image
- runs-on: ubuntu-latest
-
- steps:
- - name: checkout repo
- uses: actions/checkout@v3
-
- - name: Login as jhudsl-robot
- run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
-
- - name: Don't re-test if this is a sync branch
- run: |
- echo This was tested on OTTR_Template no need to re-run
-
- # Set up Docker build
- - name: Set up Docker Buildx
- uses: docker/setup-buildx-action@v1
-
- # Setup layer cache
- - name: Cache Docker layers
- uses: actions/cache@v2
- with:
- path: /tmp/.buildx-cache
- key: ${{ runner.os }}-buildx-${{ github.sha }}
- restore-keys: |
- ${{ runner.os }}-buildx-
-
- # Set up Docker build
- - name: Set up Docker Build
- if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
- uses: docker/setup-buildx-action@v1
-
- - name: Get token
- run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt
-
- # Build docker image
- - name: Build Docker image
- uses: docker/build-push-action@v2
- with:
- push: false
- load: true
- context: docker
- file: docker/Dockerfile
- tags: jhudsl/base_ottr
-
- # Login to Dockerhub
- - name: Login to DockerHub
- if: ${{ github.event.inputs.dockerhubpush != 'false' }}
- uses: docker/login-action@v1
- with:
- username: ${{ secrets.DOCKERHUB_USERNAME }}
- password: ${{ secrets.DOCKERHUB_TOKEN }}
-
- # Push the Docker image if set to true from a manual trigger
- - name: Push Docker image if manual trigger set to true
- if: ${{ github.event.inputs.dockerhubpush != 'false' }}
- run: |
- docker tag jhudsl/base_ottr:latest jhudsl/base_ottr:$github.event.inputs.tag
- docker push jhudsl/base_ottr:$github.event.inputs.tag
diff --git a/.github/workflows/docker-test.yml b/.github/workflows/docker-test.yml
deleted file mode 100644
index e1eab59..0000000
--- a/.github/workflows/docker-test.yml
+++ /dev/null
@@ -1,91 +0,0 @@
-
-# Candace Savonen Apr 2022
-
-name: Build Docker Image
-
-on:
- workflow_dispatch:
- inputs:
- directory:
- required: true
- type: string
- tag:
- required: true
- type: string
- dockerhubpush:
- description: 'Push to Dockerhub?'
- required: false
- default: 'false'
- type: string
- secrets:
- GH_PAT:
- required: true
- DOCKERHUB_USERNAME:
- required: false
- DOCKERHUB_TOKEN:
- required: false
-
-jobs:
-
- build-docker:
- name: Build Docker image
- runs-on: ubuntu-latest
-
- steps:
- - name: checkout repo
- uses: actions/checkout@v3
-
- - name: Verify Dockerfiles changed?
- uses: tj-actions/verify-changed-files@v8.8
- id: verify-changed-files
- with:
- files: |
- ${{ inputs.directory }}/Dockerfile
- ${{ inputs.directory }}/github_package_list.tsv
-
- - name: Login as jhudsl-robot
- run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
-
- # Set up Docker build
- - name: Set up Docker Buildx
- uses: docker/setup-buildx-action@v1
-
- # Setup layer cache
- - name: Cache Docker layers
- uses: actions/cache@v2
- with:
- path: /tmp/.buildx-cache
- key: ${{ runner.os }}-buildx-${{ github.sha }}
- restore-keys: |
- ${{ runner.os }}-buildx-
-
- - name: Set up Docker Build
- uses: docker/setup-buildx-action@v1
-
- - name: Get token
- run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt
-
- - name: Build Docker image
- uses: docker/build-push-action@v2
- with:
- push: false
- load: true
- context: ${{ inputs.directory }}
- file: ${{ inputs.directory }}/Dockerfile
- tags: ${{ inputs.tag }}
-
- # Login to Dockerhub
- - name: Login to DockerHub
- if: ${{ inputs.dockerhubpush != 'false' }}
- uses: docker/login-action@v1
- with:
- username: ${{ secrets.DOCKERHUB_USERNAME }}
- password: ${{ secrets.DOCKERHUB_TOKEN }}
-
- # Push the Docker image if set to true from a manual trigger
- - name: Push Docker image if manual trigger set to true
- if: ${{ inputs.dockerhubpush != 'false' }}
- run: docker push ${{ inputs.tag }}
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 2e122ba..d4d2515 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -139,11 +139,31 @@ jobs:
git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
shell: bash
+ # Make sure the link for AnVIL feedback is prepopulated for the specific course
+ - name: Set up feedback link
+ id: feedback
+ run: bash scripts/AnVIL_Feedback_Script.sh
+
# Run bookdown rendering
- name: Run bookdown render
id: bookdown
run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+ # Render a student guide if specified. This is a bit clunky because
+ # Bookdown does not work well if the files aren't named as such in the
+ # root directory
+ - name: Run student guide render
+ if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
+ id: student_guide
+ run: |
+ mkdir tmp1
+ mv _bookdown.yml _output.yml tmp1
+ mv student-guide/_bookdown.yml student-guide/_output.yml .
+ Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+ mv _bookdown.yml _output.yml student-guide
+ mv tmp1/_bookdown.yml tmp1/_output.yml .
+ rm -r tmp1
+
# Run TOC-less version
# Rendered content for Leanpub and Coursera is very similar.
# This job creates a shared scaffold for both.
@@ -187,15 +207,14 @@ jobs:
- name: Build components of the comment
id: build-components
run: |
- course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
+ course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
- docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
- zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+ student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx") zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
echo "zip_link=$zip_link" >> $GITHUB_OUTPUT
echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
- echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
+ echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
echo ${{steps.commit.outputs.changes}}
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 3de168a..8bb8ecb 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -10,6 +10,7 @@ on:
paths:
- '**.Rmd'
- assets/*
+ - quizzes/*
jobs:
@@ -57,7 +58,7 @@ jobs:
# We want a fresh run of the renders each time
- name: Delete old docs/*
run: rm -rf docs/*
-
+
# Make sure the link for AnVIL feedback is prepopulated for the specific course
- name: Set up feedback link
id: feedback
@@ -102,7 +103,7 @@ jobs:
git fetch origin
git add --force docs/*
git commit -m 'Render bookdown' || echo "No changes to commit"
- git pull --rebase --allow-unrelated-histories --strategy-option=ours
+ git pull --allow-unrelated-histories --strategy-option=ours
git push -u origin main || echo "No changes to push"
render-tocless:
@@ -141,7 +142,7 @@ jobs:
git fetch origin
git add --force docs/no_toc*
git commit -m 'Render toc-less' || echo "No changes to commit"
- git pull --rebase --allow-unrelated-histories --strategy-option=ours
+ git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
git push -u origin main || echo "No changes to push"
render-leanpub:
@@ -188,7 +189,7 @@ jobs:
git fetch origin
git add .
git commit -m 'Delete manuscript folder' || echo "No changes to commit"
- git pull --rebase --allow-unrelated-histories --strategy-option=ours
+ git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
git push -u origin main || echo "No changes to push"
- name: Run ottrpal::bookdown_to_embed_leanpub
@@ -218,7 +219,7 @@ jobs:
git add --force resources/*
git add --force docs/*
git commit -m 'Render Leanpub' || echo "No changes to commit"
- git pull --rebase --allow-unrelated-histories --strategy-option=ours
+ git pull --allow-unrelated-histories --strategy-option=ours
git push --force --set-upstream origin main || echo "No changes to push"
render-coursera:
diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml
index 3c3577e..dae4141 100644
--- a/.github/workflows/transfer-rendered-files.yml
+++ b/.github/workflows/transfer-rendered-files.yml
@@ -21,7 +21,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
# Use the yaml-env-action action.
- name: Load environment from YAML
@@ -42,21 +42,23 @@ jobs:
if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
steps:
+ - name: Checkout from Bookdown Repo
+ uses: actions/checkout@v4
+ with:
+ path: bookdown
+ token: ${{ secrets.GH_PAT }}
+
- name: Run git repo check
id: git_repo_check
env:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
- sudo apt-get install subversion
-
# What's the Quizzes repository's name?
QUIZ_REPO=$(echo ${GITHUB_REPOSITORY} | sed "s/_Bookdown/ /g" | sed "s/_Template/ /g" | awk '{print $1"_Quizzes"}')
echo $QUIZ_REPO
- # Get repo check script
- svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/scripts/git_repo_check.R git_repo_check.R
-
# Run repo check script
+ curl -o git_repo_check.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/git_repo_check.R
results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
echo $QUIZ_REPO exists: $results
@@ -65,8 +67,9 @@ jobs:
- name: Checkout code from Leanpub repo
if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
+ path: quizzes
repository: ${{ steps.git_repo_check.outputs.leanpub_repo }}
token: ${{ secrets.GH_PAT }}
@@ -76,17 +79,19 @@ jobs:
env:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
- # Copy over images folder
- svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/resources/chapt_screen_images resources/chapt_screen_images
+ # Copy over images folder (from bookdown to quizzes repo)
+ mkdir -p quizzes/resources/chapt_screen_images
+ cp bookdown/resources/chapt_screen_images/* quizzes/resources/chapt_screen_images
- # Copy over _bookdown.yml
- svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/_bookdown.yml _bookdown.yml
+ # Copy over _bookdown.yml (from bookdown to quizzes repo)
+ cp bookdown/_bookdown.yml quizzes/_bookdown.yml
- name: Create PR with resources files
if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
uses: peter-evans/create-pull-request@v3
id: cpr
with:
+ path: quizzes # Must create the PR in the Quizzes Repo
token: ${{ secrets.GH_PAT }}
commit-message: Copy files from Bookdown repository
signoff: false
diff --git a/_output.yml b/_output.yml
index 7d6b017..4156fd7 100644
--- a/_output.yml
+++ b/_output.yml
@@ -1,16 +1,15 @@
bookdown::gitbook:
# When using multiple css files, the default file path will be the first one #
- css: [assets/style.css, assets/AnVIL_style/anvil.css]
+ css: [assets/style.css, assets/GDSCN_style/gdscn.css]
includes:
- in_header: GA_Script.html
- before_body: assets/AnVIL_style/big-image_anvil.html
- after_body: assets/AnVIL_style/footer.html
+ before_body: assets/GDSCN_style/big-image_gdscn.html
+ after_body: assets/GDSCN_style/footer.html
highlight: tango
config:
toc:
collapse: section
before: |
- 
+ 
after: |
This content was published with bookdown by:
The Fred Hutch Data Science Lab
diff --git a/assets/style.css b/assets/style.css
index 1648b46..748acad 100755
--- a/assets/style.css
+++ b/assets/style.css
@@ -313,7 +313,6 @@ div.wip{
background-image: url("../assets/box_images/under_construction.png");
}
-
/* .book .book-body .page-wrapper .page-inner section.normal is needed
to override the styles produced by gitbook, which are ridiculously
overspecified. Goal of the selectors is to ensure internal "margins"
diff --git a/docker/Dockerfile b/docker/Dockerfile
deleted file mode 100644
index 1c0c6e0..0000000
--- a/docker/Dockerfile
+++ /dev/null
@@ -1,78 +0,0 @@
-FROM rocker/tidyverse:4.0.2
-LABEL maintainer="cansav09@gmail.com"
-WORKDIR /rocker-build/
-
-COPY install_github.R .
-
-# Install apt-getable packages to start
-RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
-RUN apt-get install -y --no-install-recommends \
- libxt6 \
- libpoppler-cpp-dev \
- vim \
- libglpk40 \
- curl \
- gpg
-
-# Install gh
-RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg;
-RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null;
-RUN apt update && apt install -y gh;
-
-# Remove old symlinks to old pandoc
-RUN unlink /usr/lib/rstudio-server/bin/pandoc/pandoc
-
-# Uninstall old version of pandoc
-RUN sudo apt-get purge pandoc pandoc-citeproc pandoc-data \
- && sudo apt-get autoremove --purge
-
-# Install pandoc
-RUN wget https://github.com/jgm/pandoc/releases/download/2.14.1/pandoc-2.14.1-1-amd64.deb \
- && sudo apt-get install ./pandoc-2.14.1-1-amd64.deb
-
-# Create new symlinks
-RUN ln -s /usr/bin/pandoc /usr/lib/rstudio-server/bin/pandoc/pandoc
-
-# Add curl, bzip2
-RUN apt-get update -qq && apt-get -y --no-install-recommends install \
- bzip2 \
- curl
-
-# Install pip3 and installation tools
-RUN apt-get -y --no-install-recommends install \
- python3-pip python3-dev
-
-# Commonly used R packages
-RUN Rscript -e "options(warn = 2);install.packages( \
- c('bookdown', \
- 'here', \
- 'leanpubr', \
- 'optparse', \
- 'oro.nifti', \
- 'qpdf', \
- 'R.utils', \
- 'rprojroot', \
- 'rgoogleslides', \
- 'servr', \
- 'spelling', \
- 'styler', \
- 'reticulate'), \
- repos = 'https://cloud.r-project.org/')"
-
-# cow needs this dependency:
-RUN Rscript -e "devtools::install_version('gitcreds', version = '0.1.1', repos = 'http://cran.us.r-project.org')"
-
-# Didactr needs this dependency:
-RUN Rscript -e "devtools::install_version('lifecycle', version = '1.0.0', repos = 'http://cran.us.r-project.org')"
-
-# Copy over git token and package list
-COPY git_token.txt .
-COPY github_package_list.tsv .
-
-# Install packages from github
-RUN Rscript install_github.R \
- --packages github_package_list.tsv \
- --token git_token.txt
-
-# Set final workdir for commands
-WORKDIR /home/rstudio
diff --git a/docker/Dockerfile_ottrpal b/docker/Dockerfile_ottrpal
deleted file mode 100644
index 692e5b7..0000000
--- a/docker/Dockerfile_ottrpal
+++ /dev/null
@@ -1,29 +0,0 @@
-FROM jhudsl/course_template:main
-LABEL maintainer="cansav09@gmail.com"
-
-# Install apt-getable packages to start
-RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
-
-RUN apt-get install -y --no-install-recommends \
- libxt6 \
- libpoppler-cpp-dev \
- vim \
- libglpk40 \
- curl \
- gpg
-
-# Install R
-RUN apt-get update && apt-get install -y r-base curl
-
-# Install R packages
-RUN Rscript -e "install.packages('curl')"
-
-# Install phantomjs
-RUN apt-get update && apt-get install build-essential chrpath libssl-dev libxft-dev -y \
- && apt-get install libfontconfig1 libfontconfig1-dev -y \
- && cd ~ && export PHANTOM_JS="phantomjs-2.1.1-linux-x86_64" \
- && wget https://github.com/Medium/phantomjs/releases/download/v2.1.1/$PHANTOM_JS.tar.bz2 \
- && sudo tar xvjf $PHANTOM_JS.tar.bz2 \
- && sudo mv $PHANTOM_JS /usr/local/share \
- && sudo ln -sf /usr/local/share/$PHANTOM_JS/bin/phantomjs /usr/local/bin \
- && phantomjs --version
diff --git a/docker/github_package_list.tsv b/docker/github_package_list.tsv
deleted file mode 100644
index e587cda..0000000
--- a/docker/github_package_list.tsv
+++ /dev/null
@@ -1,10 +0,0 @@
-rstudio/rmarkdown 02d3c2512686fda9c14c2a0e300aa02525f16ca5
-yihui/xfun 74c2a6605d8f0fb19314da542baeead6dc8697d9
-yihui/knitr a1052d12e0ff8f4ead365b4c85ef5835faa1c492
-r-lib/rlang f0c9be5c5806b4e4b120b7516f286fef3c66bda5
-jhudsl/didactr cde4598c10f2b5e2e31b47fe94ca1b02db420e10
-jhudsl/ottrpal HEAD
-tidyverse/rvest 4fe39fb5089512d77b6a9cc026e5c895258ff6ce
-R-lib/testthat e99155af85261e065192feb946dcfa6679cffae4
-rstudio/bookdown 88bc4ead8562ea281838041c795b38fc4a6a7165
-jhudsl/cow HEAD
\ No newline at end of file
diff --git a/docker/install_github.R b/docker/install_github.R
deleted file mode 100644
index fb532ec..0000000
--- a/docker/install_github.R
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env Rscript
-
-if (!"optparse" %in% installed.packages()) {
- install.packages("optparse")
-}
-
-library(optparse)
-
-################################ Set up options ################################
-# Set up optparse options
-option_list <- list(
- make_option(
- opt_str = c("-p", "--packages"), type = "character",
- default = "github_package_list.tsv" ,
- help = "Path to a TSV with a list of packages to be installed through Github,
- where file where the first column is the github package name e.g.
- jhudsl/ottrpal and the second column is the commit ID to be installed
- (to be supplied to the ref argument).
- ",
- metavar = "character"
- ),
- make_option(
- opt_str = c("--token"), type = "character",
- default = NULL,
- help = "GITHUB PAT file",
- metavar = "character"
- )
-)
-
-# Parse options
-opt <- parse_args(OptionParser(option_list = option_list))
-
-# Read in the token
-token <- as.character(readLines(opt$token)[1])
-
-# Reset GITHUB PAT to be token
-Sys.unsetenv("GITHUB_PAT")
-Sys.setenv(GITHUB_PAT = token)
-
-# set up list of packages to install
-packages <- readr::read_tsv(opt$packages,
- col_names = c("package_name", "ref"))
-
-purrr::pmap(
- packages,
- ~remotes::install_github(..1,
- auth_token = token,
- ref = ..2)
- )
-
-# Remove the file after we are done
-file.remove(opt$token)
diff --git a/index.Rmd b/index.Rmd
index 651d7c3..609285e 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -17,7 +17,7 @@ This is a companion training guide for BioDIGS, a GDSCN project that brings a re
The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home).
-{width=300px}
+{width=300px}
## Target Audience
diff --git a/resources/exclude_files.txt b/resources/exclude_files.txt
new file mode 100644
index 0000000..5525a40
--- /dev/null
+++ b/resources/exclude_files.txt
@@ -0,0 +1,8 @@
+About.Rmd
+docs/*
+style-sets/*
+manuscript/*
+CONTRIBUTING.md
+LICENSE.md
+code_of_conduct.md
+README.md
diff --git a/style-sets/AnVIL/_output.yml b/style-sets/AnVIL/_output.yml
new file mode 100644
index 0000000..7d6b017
--- /dev/null
+++ b/style-sets/AnVIL/_output.yml
@@ -0,0 +1,21 @@
+bookdown::gitbook:
+ # When using multiple css files, the default file path will be the first one #
+ css: [assets/style.css, assets/AnVIL_style/anvil.css]
+ includes:
+ in_header: GA_Script.html
+ before_body: assets/AnVIL_style/big-image_anvil.html
+ after_body: assets/AnVIL_style/footer.html
+ highlight: tango
+ config:
+ toc:
+ collapse: section
+ before: |
+
+ after: |
+ This content was published with bookdown by:
+ The Fred Hutch Data Science Lab
+ 
+ Style adapted from: rstudio4edu-book (CC-BY 2.0)
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/style-sets/AnVIL/index.Rmd b/style-sets/AnVIL/index.Rmd
new file mode 100644
index 0000000..0ae4626
--- /dev/null
+++ b/style-sets/AnVIL/index.Rmd
@@ -0,0 +1,40 @@
+---
+title: "AnVIL Book Name"
+date: "`r format(Sys.time(), '%B %d, %Y')`"
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: book.bib
+biblio-style: apalike
+link-citations: yes
+description: Description about Course/Book.
+favicon: assets/AnVIL_style/anvil_favicon.ico
+---
+
+
+# About this Book {-}
+
+This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Learn more about AnVIL by visiting https://anvilproject.org or reading the [article in Cell Genomics](https://www.sciencedirect.com/science/article/pii/S2666979X21001063).
+
+## Skills Level {-}
+
+::: {.notice}
+_Genetics_
+
+
+_Programming skills_
+
+:::
+
+## AnVIL Collection {-}
+
+Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/
+
+# Learning Objectives {-}
+
+
+
+
+
+
+
+
diff --git a/style-sets/fhdasl/_output.yml b/style-sets/fhdasl/_output.yml
index d00716f..0a86496 100644
--- a/style-sets/fhdasl/_output.yml
+++ b/style-sets/fhdasl/_output.yml
@@ -11,7 +11,8 @@ bookdown::gitbook:
before: |
after: |
- This content was published with bookdown by:
+ This content was published with bookdown using
+ The OTTR Template by:
The Fred Hutch Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
