Initial commit.

.github/workflows/publish-docker.yaml

@@ -0,0 +1,23 @@
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'Dockerfile'
+  workflow_dispatch:
+
+name: Publish Docker image
+
+jobs:
+  publish_docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Publish to Registry
+        uses: elgohr/Publish-Docker-Github-Action@v5
+        with:
+          name: ${{ github.repository }}/builder:latest
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: ghcr.io

.gitignore

@@ -0,0 +1 @@
+*.swp

Dockerfile

@@ -0,0 +1,21 @@
+FROM bioconductor/bioconductor_docker:devel
+
+RUN mkdir -p /home/rstudio/sources
+WORKDIR /home/rstudio/sources
+
+RUN R -e "BiocManager::install(c('alabaster', 'chihaya'))"
+RUN git clone https://github.com/ArtifactDB/zircon-R
+RUN git clone https://github.com/CollaboratorDB/CollaboratorDB.schemas
+RUN git clone https://github.com/CollaboratorDB/CollaboratorDB-R
+
+# Trawling through their dependencies.
+COPY install.R .
+RUN R -f install.R
+
+# Actually installing each one.
+RUN R CMD INSTALL zircon-R
+RUN R CMD INSTALL CollaboratorDB.schemas
+RUN R CMD INSTALL CollaboratorDB-R
+
+# Setting the working directory to the home.
+WORKDIR /home/rstudio

LICENSE

@@ -0,0 +1,19 @@
+Copyright 2022 Genentech Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,4 @@
+# Docker image for alabaster packages
+
+This repository provides a Docker image for using the demonstration ArtifactDB instance, known as **CollaboratorDB** (alias: "DemoDB").
+Check out [these instructions](https://github.com/CollaboratorDB/CollaboratorDB-docker/pkgs/container/CollaboratorDB-docker%2Fbuilder) for pulling the image from GitHub's container registry.

install.R

@@ -0,0 +1,17 @@
+# Loops through all source directories here and installs their dependencies.
+all.sources <- list.files()
+
+collected <- list()
+for (y in all.sources) {
+    if (!file.info(y)$isdir) {
+        next
+    }
+
+    X <- read.dcf(file.path(y, "DESCRIPTION"))
+    req <- intersect(c("Imports", "Suggests", "Depends", "LinkingTo"), colnames(X))
+    collected[[X[1,"Package"]]] <- as.character(unlist(strsplit(X[1,req], ",?\n"), use.names=FALSE))
+}
+
+all.deps <- unique(unlist(collected, use.names=FALSE))
+leftovers <- setdiff(all.deps, names(collected))
+BiocManager::install(leftovers)