Merge branch 'singularityplanemogalaxy' into 'master'

Singularityplanemogalaxy

See merge request !4

.gitlab-ci.yml

@@ -11,7 +11,7 @@ build docker-planemo:
   stage: build
   
   variables:
-    IMAGE_TAG: $CI_REGISTRY/record/docker-planemo/docker-planemo-singularity:0.74.9
+    IMAGE_TAG: $CI_REGISTRY/record/docker-planemo/singularity-planemo-galaxy:0.74.9
   
   script:
     - docker info

Dockerfile

@@ -4,7 +4,7 @@ LABEL maintainer "Patrick Chabrier <patrick.chabrier@inrae.fr>"
 
 ENV DEBIAN_FRONTEND noninteractive
 
-# Installation de singularity-ce en 3.9.2
+# Singularity-ce install in 3.9.2
 
 RUN apt-get update \
     && apt-get install -y \ 
@@ -41,12 +41,30 @@ RUN pwd \
     && make -C ./builddir \ 
     && make -C ./builddir install
 
+# Planemo install in 0.74.9
+
 RUN pip install git+https://github.com/galaxyproject/planemo.git@0.74.9
 
-ENV GALAXY_TEST_UPLOAD_ASYNC false
-ENV GALAXY_TEST_DEFAULT_INTERACTOR api
-ENV GALAXY_TEST_PORT 7777
+# Galaxy install in 21.05
 
 WORKDIR /galaxy-central
+
+RUN cd /galaxy-central \
+    && git clone -b release_21.05 https://github.com/galaxyproject/galaxy.git
+    
+RUN cd galaxy \
+    && ./run.sh start \
+    && ./run.sh stop
+
+# Dummy test to pre install somme dependencies
+
+ADD tool/dummy.xml /galaxy-central/tool/dummy.xml
+
+RUN planemo test --galaxy_root galaxy tool/dummy.xml
+
+RUN rm -rf tool*
+
+EXPOSE 9090
+
 ENTRYPOINT ["planemo"]
 CMD ["--help"]

README.md

 # docker-planemo
 
-planemo 4 SIWAA
\ No newline at end of file
+A simple container hosting planemo, singularity and a galaxy intance.
+
+# Use cases
+
+Assuming you have docker installed:
+* "Docker container list" is usefull to see what's going on.
+* "Docker container stop *CONTAINER ID*" is usefull to halt a running one.
+
+## Get the help of planemo
+
+```
+docker run registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9
+```
+
+## Get the planemo version
+
+```
+docker run registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 --version
+```
+
+## Get the singularity version
+
+```
+docker run --entrypoint="" registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 singularity --version
+```
+
+## Check the syntax of a tool
+
+Assuming you have a tool/dummy.xml in your current working folder
+
+```
+docker run -v $PWD/tool:/galaxy-central/tool registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+lint tool/dummy.xml
+```
+
+## Test a tool withe the available Galaxy
+
+Assuming :
+* you have a tool/dummy.xml in your current working folder
+* you want to test against the Galaxy instance already available inside the container
+
+
+```
+docker run -v $PWD/tool:/galaxy-central/tool registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+test  --galaxy_root galaxy \
+tool/dummy.xml
+```
+
+## Test the tool with another Galaxy version
+
+Assuming :
+* you have a tool/dummy.xml in your current working folder
+* you want to test against a specific Galaxy instance
+
+```
+docker run -v $PWD/tool:/galaxy-central/tool registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+test  --install_galaxy \
+--galaxy_branch release_21.05 \
+tool/dummy.xml
+```
+
+## Test with more feedback
+
+Assuming :
+* you have a tool/dummy.xml in your current working folder
+* you want to get the log provided
+* you want to see what has been generated
+
+```
+docker run --entrypoint="" \
+-v /tmp:/tmp -v $PWD/tool:/galaxy-central/tool \
+registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+bash -c "planemo test \
+--no_cleanup \
+--galaxy_root galaxy \
+tool/dummy.xml \
+&& cp tool_test* tool"
+```
+
+This way you get the log files inside your tool folder,
+and you can see the code generated inside /tmp
+
+## Test with mode feedback and with singularity
+
+You will need to run docker with "--privileged" and
+planemo with "--job_config_file tools/job_conf.xml",
+where singularity is enabled.
+
+```
+docker run --privileged \
+--entrypoint="" \
+-v /tmp:/tmp -v $PWD/tool:/galaxy-central/tool \
+registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+bash -c "planemo test --no_cleanup \
+--job_config_file tool/job_conf.xml \
+--galaxy_root galaxy  \
+tool/dummy.xml \
+&& cp tool_test* tool"
+```
+
+## visualize the tool inside a launched instance and play with:
+
+```
+docker run \
+-p 9090:9090 \
+--privileged \
+--entrypoint="" \
+-v /tmp:/tmp -v $PWD/tool:/galaxy-central/tool \
+registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+bash -c "planemo serve \
+--host 0.0.0.0 \
+--no_cleanup \
+--job_config_file tool/job_conf.xml \
+--galaxy_root galaxy  \
+tool/dummy.xml"
+```
+
+http://0.0.0.0:9090/ should serve galaxy an the tool tested.
+
+
+## work directly inside the container with all the convenient options
+
+```
+docker run \
+-it \
+-p 9090:9090 \
+--privileged \
+--entrypoint="" \
+-v /tmp:/tmp -v $PWD/tool:/galaxy-central/tool \
+registry.forgemia.inra.fr/record/docker-planemo/singularity-planemo-galaxy:0.74.9 \
+/bin/bash
+```
+
+
+

tool/dummy.xml

+<tool id="dummy" name="dummy" version="1.0.0">
+  <requirements>
+  </requirements>
+  <command>
+  </command>
+  <outputs>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+  </help>
+</tool>