Merge branch 'main' into cansavvy/gi_calc

.github/workflows/docker-build.yml

@@ -44,9 +44,6 @@ jobs:
       # Set up Docker build
       - name: Set up Docker Build
         uses: docker/setup-buildx-action@v1
-
-      - name: Get token
-        run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt
 
       # Build docker image
       - name: Build Docker image
@@ -70,5 +67,5 @@ jobs:
       - 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:$github.event.inputs.tag
+          docker tag hutch/gimap:latest hutch/gimap:$github.event.inputs.tag
+          docker push hutch/gimap:$github.event.inputs.tag

inst/extdata/Dockerfile

@@ -2,22 +2,14 @@ FROM rocker/tidyverse:4.0.2
 LABEL maintainer="cansav09@gmail.com"
 WORKDIR /rocker-build/
 
-COPY install_github.R .
-COPY git_token.txt .
-COPY github_package_list.tsv .
-
 # Install a package from CRAN
 RUN Rscript -e  "options(warn = 2);install.packages( \
     c('remotes', \
       'styler'), \
     repos = 'https://cloud.r-project.org/')"
 
-# Install packages from github
-RUN Rscript install_github.R \
-  --packages github_package_list.tsv \
-  --token git_token.txt
-
-
-
+# Install the thing
+RUN installGithub.r FredHutch/gimap
+
 # Set final workdir for commands
 WORKDIR /home/rstudio