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 \ ...@@ -10,15 +10,13 @@ RUN apt-get update && apt-get install -y \
docker.io \ docker.io \
wget \ wget \
curl \ curl \
libpq-dev libpq-dev \
vim
RUN git clone --depth 1 --progress https://github.com/common-workflow-language/galaxy.git /app/galaxy RUN git clone --depth 1 --progress https://github.com/common-workflow-language/galaxy.git /app/galaxy
RUN git clone --depth 1 --single-branch --branch master --progress https://github.com/hmenager/workflow-is-cwl /app/workflow-is-cwl RUN git clone --depth 1 --single-branch --branch master --progress https://github.com/EBI-metagenomics/workflow-is-cwl /app/workflow-is-cwl
RUN git clone --depth 1 --single-branch --branch assembly --progress https://github.com/hmenager/workflow-is-cwl /app/workflow-is-cwl_assembly
RUN curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add - RUN curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add -
RUN echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list RUN echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list
RUN apt-get update && apt-get install -y yarn 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/record.py /app/galaxy/lib/galaxy/model/dataset_collections/types/record.py
# init Galaxy (download deps and init DB...) # init Galaxy (download deps and init DB...)
RUN cd /app/galaxy && ./scripts/common_startup.sh RUN cd /app/galaxy && ./scripts/common_startup.sh
#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 #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 ...@@ -38,5 +36,19 @@ COPY tool_conf.xml /app/galaxy/config/tool_conf.xml
COPY welcome.html /app/galaxy/static/welcome.html COPY welcome.html /app/galaxy/static/welcome.html
# create entry point # create entry point
COPY start.sh /app/start.sh COPY start.sh /app/start.sh
# 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 create_user.py /app/galaxy/create_user.py
# copy a fixed version of workflows.py to allow Workflow API uploads until
# https://github.com/common-workflow-language/galaxy/pull/105 is merged
COPY workflows.py /app/galaxy/lib/galaxy/managers/workflows.py
# create the admin user
RUN bash -c "cd /app/galaxy && . .venv/bin/activate && python create_user.py"
# upload workflows and data
RUN git clone https://github.com/vishnubob/wait-for-it.git
RUN cd /app/galaxy && . .venv/bin/activate && pip install bioblend
COPY upload_material.py /app
COPY start_galaxy_and_upload_material.sh /app
RUN bash /app/start_galaxy_and_upload_material.sh
CMD ["sh", "/app/start.sh"] CMD ["sh", "/app/start.sh"]
EXPOSE 8080 EXPOSE 8080
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