diff toolfactory/docker/Dockerfile @ 46:f8700bed1e17 draft

Uploaded

--- a/toolfactory/docker/Dockerfile	Sun Aug 16 20:05:19 2020 -0400
+++ b/toolfactory/docker/Dockerfile	Tue Aug 18 08:25:43 2020 -0400
@@ -3,44 +3,50 @@
 # VERSION       0.2
 # patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows
 # use docker run -p 8080:80  -d -e GALAXY_AUTO_UPDATE_WORKFLOWS=/galaxy-central/workflows/TF_sample_wf.ga -v /home/ubuntu/galaxy_storage/:/export/  toolfactory
-FROM bgruening/galaxy-stable
+FROM quay.io/bgruening/galaxy:20.05
 MAINTAINER Ross Lazarus [e-mail]
 
 ENV GALAXY_CONFIG_BRAND=ToolFactory
 ENV GALAXY_LOGGING="full"
-
-# RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils
-# needed for planemo build
-
-RUN /galaxy_venv/bin/python -m pip install --upgrade pip
-# RUN /galaxy_venv/bin/python -m pip install planemo
-
+ADD tfwelcome.html /export/welcome.html
 # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'
-ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml
-ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml
+RUN mkdir -p /tftools \
+  && mkdir -p /tftools/toolfactory \
+  && mkdir -p /tftools/planemo_test
+
+ADD ./tftools/toolfactory /tftools/toolfactory
+ADD ./tftools/tf_tool_conf.xml /tftools/tf_tool_conf.xml
+ADD ./tftools/planemo_test /tftools/planemo_test
+ADD TF_example_wf.ga /tftools/TF_example_wf.ga
 
+ADD my_tool_list.yml /tftools/toolfactory_tools.yaml
+
+ENV GALAXY_AUTO_UPDATE_TOOLS=/tftools/toolfactory_tools.yaml
+# NOTE above does work but takes 1-2 minutes
+
+# ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/tf_tool_conf.xml,config/shed_tool_conf.xml.sample
+#ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=/tftools/tf_tool_conf.xml,config/tool_conf.xml.sample
+# works but does not install dependencies
 # Add workflows to the Docker image
-RUN mkdir -p $GALAXY_ROOT/workflows
-ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga
+
+ENV $GALAXY_DEFAULT_ADMIN_USER="admin"
+# ensure triggering post-start-actions.sh
+
+ADD tftools/datatypes_conf.xml $GALAXY_ROOT/conf/datatypes_conf.xml.sample
 ADD post-start-actions.sh /export/post-start-actions.sh
+ADD post-start-actions.sh $GALAXY_ROOT/config/post-start-actions.sh
+
 RUN chmod a+xr /export/post-start-actions.sh \
- && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga 
-
+ && chmod a+xr /tftools/TF_example_wf.ga \
+ && chmod a+xr $GALAXY_ROOT/config/post-start-actions.sh
 # Add Galaxy interactive tours
 # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/
 # Add data library definition file
 # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
-# cleanup dance
-RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \
-    && find $GALAXY_ROOT/ -name '*.pyc' -delete | true \
-    && find /usr/lib/ -name '*.pyc' -delete | true \
-    && find /var/log/ -name '*.log' -delete | true \
-    && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \
-    && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm
-ENV GALAXY_DEFAULT_ADMIN_USER=''
-VOLUME ["/export/"]
+
+VOLUME ["/export/", "/data/", "/var/lib/docker"]
 EXPOSE :80
 EXPOSE :21
 EXPOSE :8800
+
 CMD ["/usr/bin/startup"]
-