Flag Dockerfile workarounds as TEMPORARY and trim verbosity

The Dockerfiles in this repo are meant to be readable as teaching
material. Shorten the renderValue-patch and CMD comments to match the
density of the other branches' Dockerfiles, and prefix each fix with
TEMPORARY: linking the upstream shinyngs PR that will obsolete them.

Also drop redundant library(DT) and library(plotly) from CMD — the
sed patch is the primary fix for the widget race; the htmlwidget
resource paths are registered lazily by Shiny when an output is
rendered, no library() call required.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: pinin4fjords

.seqera/Dockerfile

@@ -41,21 +41,20 @@ RUN rm -rf /opt/conda/pkgs/*.lock && \
     && micromamba clean --all --yes \
     && rm -rf /opt/conda/pkgs/*.lock
 
-# ---------------------------------------------------------------
-# Workaround: htmlwidgets 1.6.4's Shiny binding calls the synchronous
-# Shiny.renderDependencies(data.deps) before bindingDef.renderValue, so
-# the widget plugin <script> tag is appended but not awaited. Locally
-# that's a <1ms race; behind the Seqera Studios iframe/connect-client
-# relay it consistently loses, so e.g. $().DataTable is undefined when
-# the DT binding tries to initialise the table. Patch to use the
-# async variant and await it.
+# TEMPORARY: async-patch htmlwidgets 1.6.4 shinyBinding.renderValue so
+# widget plugins load before the binding runs. Drop once
+# https://github.com/pinin4fjords/shinyngs/pull/92 ships via bioconda.
 RUN f=/opt/conda/envs/shinyngs/lib/R/library/htmlwidgets/www/htmlwidgets.js \
- && grep -q 'shinyBinding.renderValue = function(el, data)' "$f" \
- && sed -i \
-      -e 's|shinyBinding\.renderValue = function(el, data) {|shinyBinding.renderValue = async function(el, data) {|' \
-      -e 's|Shiny\.renderDependencies(data\.deps);|await (Shiny.renderDependenciesAsync ? Shiny.renderDependenciesAsync(data.deps) : Shiny.renderDependencies(data.deps));|' \
-      "$f" \
- && grep -n 'await (Shiny.renderDependenciesAsync' "$f"
+ && if grep -q 'await (Shiny.renderDependenciesAsync' "$f"; then \
+      echo "htmlwidgets.js already patched, skipping"; \
+    elif grep -q 'shinyBinding\.renderValue = function(el, data)' "$f"; then \
+      sed -i \
+        -e 's|shinyBinding\.renderValue = function(el, data) {|shinyBinding.renderValue = async function(el, data) {|' \
+        -e 's|Shiny\.renderDependencies(data\.deps);|await (Shiny.renderDependenciesAsync ? Shiny.renderDependenciesAsync(data.deps) : Shiny.renderDependencies(data.deps));|' \
+        "$f"; \
+    else \
+      echo "ERROR: htmlwidgets.js renderValue pattern not found" >&2; exit 1; \
+    fi
 
 # Add connect-client version label for Platform capability tracking
 ARG CONNECT_CLIENT_VERSION
@@ -74,10 +73,7 @@ COPY app.R data.rds /app/
 # ---------------------------------------------------------------
 ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]
 
-# The port is set by the CONNECT_TOOL_PORT environment variable.
-# shinyngs must be attached before app.R is sourced (app.R calls
-# prepareApp() without namespacing it). DT, shinyBS, plotly, shinyjs
-# are also attached so their Shiny resource paths register with httpuv,
-# otherwise widget JS/CSS (e.g. jquery.dataTables.min.js, sbs/shinyBS.css)
-# 404 and tables/plots fail to render.
-CMD ["micromamba", "run", "-n", "shinyngs", "R", "-e", "library(shinyngs); library(DT); library(shinyBS); library(plotly); library(shinyjs); shiny::runApp('/app', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"]
+# Port is set by CONNECT_TOOL_PORT. library() calls are required:
+# shinyngs attaches prepareApp() for app.R; shinyBS/shinyjs register
+# their addResourcePath hooks (else sbs/shinyBS.css etc. 404).
+CMD ["micromamba", "run", "-n", "shinyngs", "R", "-e", "library(shinyngs); library(shinyBS); library(shinyjs); library(markdown); shiny::runApp('/app', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"]

README.md

@@ -19,6 +19,16 @@ a standalone Shiny application in Seqera Platform.
 5. Select your compute environment
 6. Click **Add** then **Start**
 
+### Alternative: Use Pre-built Image
+
+```
+ghcr.io/seqeralabs/custom-studios-examples/shinyngs:latest
+```
+
+Published automatically by `.github/workflows/build.yml` on every push to this
+branch. `:latest` tracks the branch head; individual builds are also tagged
+with the short commit SHA.
+
 ### Alternative: Build with Wave CLI
 
 ```bash
@@ -40,25 +50,39 @@ docker run --rm --platform=linux/amd64 \
   --entrypoint micromamba \
   shinyngs-studio \
   run -n shinyngs R -e \
-  "shiny::runApp('/app', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"
+  "library(shinyngs); library(shinyBS); library(shinyjs); library(markdown); shiny::runApp('/app', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"
 ```
 
 Then open http://localhost:3838.
 
 ## What's in the image
 
-- `r-shinyngs` from Bioconda, installed into a micromamba env named `shinyngs`
+- `r-shinyngs` and `r-markdown` from Bioconda/conda-forge, installed into a
+  micromamba env named `shinyngs`
 - `connect-client` 0.12 for Studios session bootstrapping
-- A baked-in RNA-seq demo app generated at build time from the bundled
-  `SRP254919` test dataset via `shinyngs`'s `make_app_from_files.R`, producing
-  `/app/app.R` and `/app/data.rds`
+- A pre-built shinyngs app for the `SRP254919` RNA-seq test dataset
+  (`/app/app.R` + `/app/data.rds`, produced upstream with
+  `shinyngs::make_app_from_files.R`)
+
+## Temporary workarounds
+
+The Dockerfile carries two small fixes flagged as `TEMPORARY:` that make
+standalone Shiny apps render correctly behind the Studios iframe +
+connect-client relay (attaching `shinyBS`/`shinyjs` so their resource paths
+register, and patching `htmlwidgets.js` to await plugin scripts before the
+widget binding runs). Both go away once
+[pinin4fjords/shinyngs#92](https://github.com/pinin4fjords/shinyngs/pull/92)
+ships via bioconda; the sed step is idempotent and will skip automatically
+when upstream is already async.
 
 ## Customising the data
 
-To swap in your own dataset, replace the files under `.seqera/` with your own
-expression matrix, sample metadata, feature metadata, contrasts, and
-differential-results TSVs, then rebuild. See `shinyngs`'s
-`make_app_from_files.R --help` for input schema.
+The app is built from five TSVs/CSVs fed to `shinyngs::make_app_from_files.R`
+(expression matrix, sample metadata, feature metadata, contrasts,
+differential-results). To swap in your own dataset, regenerate `app.R` +
+`data.rds` on any machine with `r-shinyngs` installed and replace the files
+under `.seqera/`, then rebuild. See `make_app_from_files.R --help` for the
+full input schema.
 
 ## References