Commit 2523e2fb authored by Hervé  MENAGER's avatar Hervé MENAGER
Browse files

modify the Dockerfile to include all new material

parent 17d9987e
Pipeline #12584 passed with stages
in 12 minutes and 16 seconds
......@@ -10,15 +10,13 @@ RUN apt-get update && apt-get install -y \ \
wget \
curl \
libpq-dev \
RUN git clone --depth 1 --progress /app/galaxy
RUN git clone --depth 1 --single-branch --branch master --progress /app/workflow-is-cwl
RUN git clone --depth 1 --single-branch --branch assembly --progress /app/workflow-is-cwl_assembly
RUN git clone --depth 1 --single-branch --branch master --progress /app/workflow-is-cwl
RUN curl -sS | apt-key add -
RUN echo "deb stable main" | tee /etc/apt/sources.list.d/yarn.list
RUN apt-get update && apt-get install -y yarn
#quickfix due to record not being in the right folder following rebase (04/03/2019)
RUN mv /app/galaxy/lib/galaxy/dataset_collections/types/ /app/galaxy/lib/galaxy/model/dataset_collections/types/
# init Galaxy (download deps and init DB...)
RUN cd /app/galaxy && ./scripts/
#RUN cd /app/galaxy && . .venv/bin/activate && cwltool --pack /app/workflow-is-cwl/tools/Diamond/Diamon.blastx-v0.9.21.cwl > /app/workflow-is-cwl/tools/Diamond/Diamon.blastx-v0.9.21.packed.cwl
......@@ -38,5 +36,19 @@ COPY tool_conf.xml /app/galaxy/config/tool_conf.xml
COPY welcome.html /app/galaxy/static/welcome.html
# create entry point
COPY /app/
# test modified gx annotation for type
COPY Diamon.makedb-v0.9.21.cwl /app/workflow-is-cwl/tools/Diamond/Diamon.makedb-v0.9.21.cwl
COPY /app/galaxy/
# copy a fixed version of to allow Workflow API uploads until
# is merged
COPY /app/galaxy/lib/galaxy/managers/
# create the admin user
RUN bash -c "cd /app/galaxy && . .venv/bin/activate && python"
# upload workflows and data
RUN git clone
RUN cd /app/galaxy && . .venv/bin/activate && pip install bioblend
COPY /app
COPY /app
RUN bash /app/
CMD ["sh", "/app/"]
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