more compatibility work

Dockerfile

@@ -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

README.md

@@ -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: