From 23cd01cd884cfede7caecee66a9f5d746f6c4a83 Mon Sep 17 00:00:00 2001
From: Nick Wiltsie <nwiltsie@users.noreply.github.com>
Date: Fri, 16 Aug 2024 13:12:43 -0700
Subject: [PATCH] Update tool-Docker-action to v2.1.0 (#21)

* Update tool-Docker-action to v2.1.0

* Switch to rocker/r-ver for better stability

* Strip out library installation directives
---
 .github/workflows/Docker-build-release.yaml | 20 ------------
 .github/workflows/docker-build-release.yaml | 36 +++++++++++++++++++++
 Dockerfile                                  | 12 +++----
 installer.R                                 | 11 +------
 4 files changed, 41 insertions(+), 38 deletions(-)
 delete mode 100644 .github/workflows/Docker-build-release.yaml
 create mode 100644 .github/workflows/docker-build-release.yaml

diff --git a/.github/workflows/Docker-build-release.yaml b/.github/workflows/Docker-build-release.yaml
deleted file mode 100644
index b2313d4..0000000
--- a/.github/workflows/Docker-build-release.yaml
+++ /dev/null
@@ -1,20 +0,0 @@
----
-on:
-  push:
-    branches: ['main']
-    tags: ['v*']
-  release:
-    types: [published]
-
-jobs:
-  build-and-push-image:
-    runs-on: ubuntu-latest
-    name: A job to build and push a docker image
-    permissions:
-      contents: read
-      packages: write
-    steps:
-      - id: build-push
-        uses: uclahs-cds/tool-Docker-action/build-release@latest
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/docker-build-release.yaml b/.github/workflows/docker-build-release.yaml
new file mode 100644
index 0000000..40ae5da
--- /dev/null
+++ b/.github/workflows/docker-build-release.yaml
@@ -0,0 +1,36 @@
+---
+name: Update image in GHCR
+
+run-name: >
+  ${{
+    github.event_name == 'delete' && format(
+      'Delete `{0}{1}`',
+      github.event.ref_type == 'branch' && 'branch-' || '',
+      github.event.ref
+    )
+    || github.ref == 'refs/heads/main' && 'Update `dev`'
+      || format(
+        'Update `{0}{1}`',
+        !startsWith(github.ref, 'refs/tags') && 'branch-' || '',
+        github.ref_name
+      )
+  }} docker tag
+
+on:
+  push:
+    branches-ignore: ['gh-pages']
+    tags: ['v*']
+  delete:
+
+jobs:
+  push-or-delete-image:
+    runs-on: ubuntu-latest
+    name: Update GitHub Container Registry
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: uclahs-cds/tool-Docker-action@v2.1.0
+      # Uncomment if you expect to use non-SemVer release tags
+      # with:
+      #   non-semver-tags: true
diff --git a/Dockerfile b/Dockerfile
index 4f368ad..c8a6cb1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,8 +13,7 @@ RUN mamba create -qy -p /usr/local \
     cancerit-allelecount==${ALLELECOUNT_VERSION} \
     impute2==${IMPUTE2_VERSION}
 
-FROM ubuntu:20.04
-FROM r-base:4.4.1
+FROM rocker/r-ver:4.4.1
 COPY --from=builder /usr/local /usr/local
 
 RUN apt-get update \
@@ -40,23 +39,20 @@ ARG ASCAT="VanLoo-lab/ascat/ASCAT@v${ASCAT_VERSION}"
 ARG COPYNUMBER="igordot/copynumber@${COPYNUMBER_VERSION}"
 ARG BATTENBERG="Wedge-lab/battenberg@v${BATTENBERG_VERSION}"
 
-# R library path to install the above packages
-ARG LIBRARY="/usr/lib/R/site-library"
-
 # Install Package Dependency toolkit
-RUN library=${LIBRARY} R -e 'install.packages(c("argparse", "BiocManager", "pkgdepends", "optparse"), lib = Sys.getenv("library"))' && \
+RUN R -e 'install.packages(c("argparse", "BiocManager", "pkgdepends", "optparse"))' && \
     R -q -e 'BiocManager::install(c("ellipsis", "splines", "VariantAnnotation"))'
 
 # Install Battenberg
 COPY installer.R /usr/local/bin/installer.R
 RUN chmod +x /usr/local/bin/installer.R
 
-RUN Rscript /usr/local/bin/installer.R -l ${LIBRARY} -d ${COPYNUMBER} ${ASCAT} ${BATTENBERG}
+RUN Rscript /usr/local/bin/installer.R -d ${COPYNUMBER} ${ASCAT} ${BATTENBERG}
 
 # Modify paths to reference files
 COPY modify_reference_path.sh /usr/local/bin/modify_reference_path.sh
 RUN chmod +x /usr/local/bin/modify_reference_path.sh && \
-    bash /usr/local/bin/modify_reference_path.sh /usr/lib/R/site-library/Battenberg/example/battenberg_wgs.R /usr/local/bin/battenberg_wgs.R
+    bash /usr/local/bin/modify_reference_path.sh /usr/local/lib/R/site-library/Battenberg/example/battenberg_wgs.R /usr/local/bin/battenberg_wgs.R
 
 RUN ln -sf /usr/local/lib/R/site-library/Battenberg/example/filter_sv_brass.R /usr/local/bin/filter_sv_brass.R && \
     ln -sf /usr/local/lib/R/site-library/Battenberg/example/battenberg_cleanup.sh /usr/local/bin/battenberg_cleanup.sh
diff --git a/installer.R b/installer.R
index b30c810..4c9f491 100644
--- a/installer.R
+++ b/installer.R
@@ -3,11 +3,6 @@ library(pkgdepends);
 
 parser <- ArgumentParser();
 
-parser$add_argument(
-    '-l',
-    '--lib',
-    help = 'Library path to install the tools'
-    );
 parser$add_argument(
     '-d',
     '--dependencies',
@@ -18,12 +13,8 @@ parser$add_argument(
 args <- parser$parse_args();
 
 tools <- args$dependencies;
-lib <- args$lib;
 
-pkg.installation.proposal <- new_pkg_installation_proposal(
-    tools,
-    config = list(library = lib)
-    );
+pkg.installation.proposal <- new_pkg_installation_proposal(tools);
 pkg.installation.proposal$solve();
 pkg.installation.proposal$download();
 pkg.installation.proposal$install();