Commit 78f1f2ce authored by Hervé  MENAGER's avatar Hervé MENAGER

more compatibility work

parent 004a93ec
Pipeline #11373 failed with stages
in 9 minutes and 57 seconds
......@@ -11,7 +11,6 @@ RUN apt-get update && apt-get install -y \
wget \
curl \
libpq-dev
#RUN git clone --depth 1 --progress https://github.com/hmenager/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 assembly --progress https://github.com/hmenager/workflow-is-cwl /app/workflow-is-cwl_assembly
......@@ -20,18 +19,25 @@ RUN echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources
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 && ls database/*
#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 && ./create_db.sh
RUN cd /app/galaxy && ./manage_db.sh upgrade
# DEBUG complex types
COPY representation.py /app/galaxy/lib/galaxy/tools/cwl/representation.py
COPY parser.py /app/galaxy/lib/galaxy/tools/cwl/parser.py
#COPY __init__.py /app/galaxy/lib/galaxy/tools/__init__.py
COPY process.py /app/galaxy/.venv/local/lib/python2.7/site-packages/cwltool/process.py
COPY wrappers.py /app/galaxy/lib/galaxy/tools/wrappers.py
COPY TransDecoder.LongOrfs-v5.cwl /app/workflow-is-cwl/tools/TransDecoder/TransDecoder.LongOrfs-v5.cwl
# local config
COPY job_conf.xml /app/galaxy/config/job_conf.xml
COPY dependency_resolvers_conf.xml /app/galaxy/config/dependency_resolvers_conf.xml
COPY galaxy.yml /app/galaxy/config/galaxy.yml
#COPY tool_conf_test.xml /app/galaxy/config/tool_conf.xml
#COPY concatenate.cwl /app/galaxy/tools/
#COPY concatenate-docker.cwl /app/galaxy/tools/
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
CMD ["sh", "/app/start.sh"]
EXPOSE 8080
......@@ -9,7 +9,7 @@ docker build . -t galaxycwlis
run server locally:
```bash
docker run -i -t -p 8080:8080 -v /var/run/docker.sock:/var/run/docker.sock galaxycwlis:latest
docker run --privileged -i -t -p 8080:8080 galaxycwlis:latest
```
open terminal in server:
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