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chore: make compatible with git integration and Wave build #39

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Merged
weronikasosnowskaseqera merged 1 commit into from
Jun 23, 2026
Merged

chore: make compatible with git integration and Wave build #39

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5 changes: 5 additions & 0 deletions .seqera/.dockerignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
# data.rds is delivered at runtime via the Studios git clone (into
# /workspace/.seqera), not through the image build context. It also
# exceeds the 5MB per-file build-context limit, so it must be excluded
# here or the studio build will fail.
data.rds
19 changes: 14 additions & 5 deletions .seqera/Dockerfile
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Expand Up @@ -77,10 +77,17 @@ LABEL io.seqera.connect.version="${CONNECT_CLIENT_VERSION}"
COPY --from=connect /usr/bin/connect-client /usr/bin/connect-client
RUN /usr/bin/connect-client --install

WORKDIR /app

# Pre-built shinyngs app and its serialised dataset
COPY app.R data.rds /app/
# ---------------------------------------------------------------
# App code (app.R) and dataset (data.rds) are NOT copied into the
# image. They are delivered at runtime by the Studios git clone into
# /workspace/.seqera (configured via session.clone in studio-config.yaml).
#
# WARNING: If clone is not enabled, the studio won't run — app.R and
# data.rds will be missing from the container.
#
# data.rds is also excluded from the docker build context via
# .seqera/.dockerignore (it exceeds the 5MB build-context file limit).
# ---------------------------------------------------------------

# ---------------------------------------------------------------
# 3) Launch with connect-client --entrypoint (for Platform)
Expand All @@ -90,4 +97,6 @@ ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]
# 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')))"]
# runApp() runs from the cloned app dir, so app.R's relative
# readRDS("data.rds") resolves to /workspace/.seqera/data.rds.
CMD ["micromamba", "run", "-n", "shinyngs", "R", "-e", "library(shinyngs); library(shinyBS); library(shinyjs); library(markdown); shiny::runApp('/workspace/.seqera', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"]
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