Adding Docker building and galaxy wrapping GHA (#1)

* Add shiny Dockerfile

.github/scripts/galaxy-wrapper-template.xml

@@ -0,0 +1,27 @@
+<tool id="interactivetool_biocshiny_{{{ID}}}" tool_type="interactive" name="{{{NAME}}}" version="0.1">
+    <description>{{{NAME}}} BiocShiny App</description>
+    <requirements>
+        <container type="docker">{{{CONTAINER}}}</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="{{{ID}}}" requires_domain="True">
+            <port>3838</port>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+    </environment_variables>
+    <command detect_errors="aggressive">/init</command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        This is an auto-generated wrapper for a BiocShiny application. See source and report issues at {{{SOURCE}}}.
+    </help>
+</tool>

.github/workflows/build_container.yaml

@@ -0,0 +1,62 @@
+name: Build shiny Docker image and generate Galaxy wrapper
+on:
+  workflow_dispatch: {}
+  push: {}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Extract metadata for container image
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=raw,value={{branch}}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          platforms: linux/amd64
+
+      - name: Login to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push container image to ghcr
+        uses: docker/build-push-action@v4
+        with:
+          file: Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64
+
+      - name: Set variables
+        id: vars
+        run: |
+          echo "container=${{ steps.meta.outputs.tags }}" >> $GITHUB_OUTPUT
+          echo "source=https://github.com/${{github.repository}}" >> $GITHUB_OUTPUT
+          NAME="$(echo '${{github.repository}}' | awk -F'/' '{print $2}')"
+          echo "name=$NAME" >> $GITHUB_OUTPUT
+          echo "id=$(echo $NAME | tr '[:upper:]' '[:lower:]')" >> $GITHUB_OUTPUT
+
+      - name: Generate wrapper
+        run: |
+          cp .github/scripts/galaxy-wrapper-template.xml galaxy-wrapper.xml
+          sed -i 's#{{{CONTAINER}}}#${{steps.vars.outputs.container}}#g' galaxy-wrapper.xml
+          sed -i 's#{{{SOURCE}}}#${{steps.vars.outputs.source}}#g' galaxy-wrapper.xml
+          sed -i 's#{{{NAME}}}#${{steps.vars.outputs.name}}#g' galaxy-wrapper.xml
+          sed -i 's#{{{ID}}}#${{steps.vars.outputs.id}}#g' galaxy-wrapper.xml
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add galaxy-wrapper.xml
+          git commit -m "Update Galaxy Wrapper $(TZ=EST date '+%Y-%m-%d_%H-%M')"
+          git push

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BiocWorkshopSubmit
 Type: Package
 Title: Provides a shiny app for workshop submissions
-Version: 0.99.8
+Version: 0.99.9
 Authors@R: person(
   "Marcel", "Ramos", , "[email protected]",
   c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")

Dockerfile

@@ -0,0 +1,14 @@
+FROM ghcr.io/bioconductor/shiny:devel as build
+
+RUN chown -R shiny /usr/local/lib/R/site-library && chown -R shiny /usr/local/lib/R/library && rm -rf /srv/shiny-server/sample-apps && curl -o /srv/shiny-server/index.html https://gist.githubusercontent.com/almahmoud/58261d03bfb342274f2e642c4b2ebc4d/raw/4e0271990bce57ae091f622db47b15f8fd89fa29/index.html && mkdir -p /srv/shiny-server/biocshiny && sed -i '/^run_as shiny;/a app_init_timeout 300;\napp_idle_timeout 300;' /etc/shiny-server/shiny-server.conf
+
+COPY --chown=shiny:shiny . /tmp/repo/
+
+USER shiny
+
+RUN cd /tmp/repo && Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)" && Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())" && rm -rf /tmp/repo
+
+COPY --chown=shiny:shiny app.R /srv/shiny-server/biocshiny/app.R
+
+USER root
+

R/BiocWorkshopSubmit.R

@@ -5,8 +5,8 @@
     '## READ ONLY: DO NOT EDIT ##',
     '/request', 'id="{{id}}"', 'title="{{title}}"',
     'description="{{description}}"', 'section="{{section}}"',
-    'startfile="{{startfile}}"', 'source="https://github.com/{{ghrepo}}"',
-    'docker="{{url}}:{{tag}}"'
+    'startfile="{{startfile}}"', 'source="{{gitrepo}}"',
+    'docker="{{url}}:{{tag}}"', 'pkglist="{{pkglist}}"', 'vignettes="{{vignettes}}"'
 )
 
 .ISSUE_GH_REPO <- "Bioconductor/workshop-contributions"
@@ -43,9 +43,9 @@ appCSS <- paste(
 #'
 #' @export
 BiocWorkshopSubmit <- function(...) {
-    fieldsMandatory <- c("id", "title", "section", "ghrepo", "url")
+    fieldsMandatory <- c("id", "title", "section")
     fieldsAll <- c("id", "title", "description", "section",
-        "startfile", "ghrepo", "url", "tag")
+        "startfile", "gitrepo", "url", "tag", "pkglist", "vignettes")
     ui <- fluidPage(
         useShinyjs(),
         inlineCSS(appCSS),
@@ -100,19 +100,21 @@ BiocWorkshopSubmit <- function(...) {
                                 ## TODO: point out workshop.bioconductor.org examples
                                 textInput("description", "Description"),
                                 textInput(
-                                    "ghrepo",
-                                    label = mandatory("GitHub Repository"),
-                                    placeholder = "username/repository"
+                                    "gitrepo",
+                                    label = "Git Repository",
+                                    placeholder = "https://github.com/username/repository"
                                 ),
                                 textInput(
                                     "startfile", "Start File", value = "README.md"
                                 ),
                                 textInput(
                                     "url",
-                                    label = mandatory("Container URL"),
+                                    label = "Container URL",
                                     placeholder = "ghcr.io/username/repo"
                                 ),
-                                textInput("tag", "Container Tag", value = "latest"),
+                                textInput("tag", "Container Tag", placeholder = "devel"),
+                                textInput("pkglist", "Packages to pre-install", placeholder="S4Vectors,username/repo,GenomicRanges"),
+                                textInput("vignettes", "Vignettes to add to container (comma sep.)", placeholder="Relative paths to vignettes or URL list e.g., vignettes/workshop.Rmd OR https://gist.githubusercontent.com/user/repo/vignettes/workshop.Rmd"),
                                 actionButton("render", "Render", class = "btn-primary")
                             ),
                             hr(),
@@ -181,9 +183,9 @@ BiocWorkshopSubmit <- function(...) {
 
     server <- function(input, output, session) {
         observeEvent(input$presubmit, {
-            ghrepo <- input[["prepop"]]
-            updateTextInput(session, "ghrepo", value = ghrepo)
-            descfile <- read_gh_file(ghrepo)
+            gitrepo <- paste0("https://github.com/", input[["prepop"]])
+            updateTextInput(session, "gitrepo", value = gitrepo)
+            descfile <- read_gh_file(input[["prepop"]])
             title <- descfile[, "Title"]
             updateTextInput(session, "title", value = unname(title))
             description <- .parse_description(descfile)

R/utils.R

@@ -55,7 +55,7 @@ create_gh_issue <- function(ghrepo, title, body) {
 }
 
 add_comment_gh_issue <- function(ghrepo, title, body, issue_number) {
-    ghrepo <- unlist(strsplit(ghrepo, "/", fixed = TRUE))
+    ghrepo <- tail(unlist(strsplit(ghrepo, "/", fixed = TRUE)), 2L)
     names(ghrepo) <- c("owner", "repo")
     gh(
         "POST /repos/{owner}/{repo}/issues/{issue_number}/comments",

galaxy-wrapper.xml

@@ -0,0 +1,27 @@
+<tool id="interactivetool_biocshiny_biocworkshopsubmit" tool_type="interactive" name="BiocWorkshopSubmit" version="0.1">
+    <description>BiocWorkshopSubmit BiocShiny App</description>
+    <requirements>
+        <container type="docker">ghcr.io/almahmoud/biocworkshopsubmit:devel</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="biocworkshopsubmit" requires_domain="True">
+            <port>3838</port>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key" />
+    </environment_variables>
+    <command detect_errors="aggressive">/init</command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+        This is an auto-generated wrapper for a BiocShiny application. See source and report issues at https://github.com/almahmoud/BiocWorkshopSubmit.
+    </help>
+</tool>