modify the Dockerfile to include all new material

Dockerfile

@@ -10,15 +10,13 @@ RUN apt-get update && apt-get install -y \
   docker.io \
   wget \
   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 --single-branch --branch master --progress https://github.com/hmenager/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 git clone --depth 1 --single-branch --branch master --progress https://github.com/EBI-metagenomics/workflow-is-cwl /app/workflow-is-cwl
 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 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...)
 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
@@ -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 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"]
 EXPOSE 8080