Diffusion eSCT pipeline interoperability e956cc851379

Created public branch with re-organised files
e956cc851379
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Authored by laurenczy on Jun 30 2017, 15:09.

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Created public branch with re-organised files

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Committed

laurenczy

Jun 30 2017, 15:09

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laurenczy

Jun 30 2017, 15:10

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R2915:41139a0fa5b1: Added config file for hello_world

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laurenczy committed R2915:e956cc851379: Created public branch with re-organised files (authored by laurenczy).Jun 30 2017, 15:09

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		Path
D		SIS
D		SIS/docker2singularity-master
D		SIS/docker2singularity-master/Dockerfile
D		SIS/docker2singularity-master/LICENSE
D		SIS/docker2singularity-master/README.md
D		SIS/docker2singularity-master/docker2singularity.sh
D		SIS/hello_world_pipeline
D		SIS/hello_world_pipeline/.dockerignore
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/Dockerfile
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/README.txt
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/create_and_run_container_locally.sh
V	(dir)	{SIS/hello_world_pipeline/data/ → example_pipelines/hello_world/data}
V	(dir)	{SIS/hello_world_pipeline/data/ref_output/ → example_pipelines/hello_world/data/ref_output}
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/content.md5
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/hello_0.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/hello_1.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/hello_2.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/hello_3.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/helloworld_0.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/helloworld_1.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/helloworld_2.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/helloworld_3.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/world_0.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/world_1.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/world_2.log
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/data/ref_output/world_3.log
V	(dir)	{SIS/hello_world_pipeline/pipeline/ → example_pipelines/hello_world/pipeline}
V		{SIS/hello_world_pipeline → example_pipelines/hello_world}/pipeline/hello_world_pipeline.snake
D		SIS/hello_world_pipeline_light
D		SIS/hello_world_pipeline_light/.dockerignore
D		SIS/hello_world_pipeline_light/Dockerfile
D		SIS/hello_world_pipeline_light/README.txt
D		SIS/hello_world_pipeline_light/create_and_run_container_locally.sh
D		SIS/hello_world_pipeline_light/pipeline
D		SIS/hello_world_pipeline_light/pipeline/hello_world_pipeline.snake
D		SIS/scicore_pipeline1_LSF
D		SIS/scicore_pipeline1_LSF/.dockerignore
D		SIS/scicore_pipeline1_LSF/Dockerfile
D		SIS/scicore_pipeline1_LSF/LSF_submit-script-with-containers.sh
D		SIS/scicore_pipeline1_LSF/config.yaml
D		SIS/scicore_pipeline1_LSF/create_and_run_container_locally.sh
D		SIS/scicore_pipeline1_LSF/scicore_pipeline1.snake
D		SIS/scicore_pipeline2_LSF
D		SIS/scicore_pipeline2_LSF/.dockerignore
D		SIS/scicore_pipeline2_LSF/Dockerfile
D		SIS/scicore_pipeline2_LSF/LSF_submit-script-with-containers.sh
V		{SIS/scicore_pipeline2_LSF/Singularity → singularity-pipeline-runner/bioinformatics_pipeline2.singularity}
D		SIS/scicore_pipeline2_LSF/create_and_run_container_locally.sh
D		SIS/test_runner_script
V		{SIS/test_runner_script → singularity-pipeline-runner}/.gitignore
V		{SIS/test_runner_script → singularity-pipeline-runner}/cowsay.yaml
V		{SIS/test_runner_script → example_pipelines/hello_world}/hello_world.yaml
D		SIS/test_runner_script/pipeline.py
D		UniBe
D		UniBe/.gitignore
D		UniBe/Pipeline2
V		{UniBe → singularity-pipeline-runner}/README.md
V		{UniBe → singularity-pipeline-runner}/pipeline.py
V		{UniBe/pipeline.yaml → singularity-pipeline-runner/hello_world.yaml}
V		{UniBe → singularity-pipeline-runner}/requirements.txt
V		{UniBe/scicore-pipeline-2a.yaml → singularity-pipeline-runner/bioinformatics_pipeline2.yaml}
V		{UniBe → singularity-pipeline-runner}/slurm-submit-script-WITH-containers.sh
D		Vital-IT
D		Vital-IT/bsub-docker-singularity-pipeline1.sh
D		Vital-IT/bsub-docker-singularity-pipeline2.sh
D		Vital-IT/prepare-pipeline1.sh
D		Vital-IT/prepare-pipeline2.sh
A	(dir)	example_pipelines/
V	(dir)	{example_pipelines/bioinformatics_pipeline2/ ← sciCORE/pipeline2}
V		{example_pipelines/bioinformatics_pipeline2 ← sciCORE/pipeline2}/README.txt
V		{example_pipelines/bioinformatics_pipeline2 ← sciCORE/pipeline2}/Singularity
V		{example_pipelines/bioinformatics_pipeline2 ← sciCORE/pipeline2}/slurm-submit-script-WITH-containers.sh
V		{example_pipelines/bioinformatics_pipeline2 ← sciCORE/pipeline2}/slurm-submit-script-WITHOUT-containers.sh
A	(dir)	example_pipelines/hello_world/
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/Dockerfile
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/README.txt
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/create_and_run_container_locally.sh
V	(dir)	{example_pipelines/hello_world/data/ ← SIS/hello_world_pipeline/data}
V	(dir)	{example_pipelines/hello_world/data/ref_output/ ← SIS/hello_world_pipeline/data/ref_output}
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/content.md5
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/hello_0.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/hello_1.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/hello_2.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/hello_3.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/helloworld_0.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/helloworld_1.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/helloworld_2.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/helloworld_3.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/world_0.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/world_1.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/world_2.log
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/data/ref_output/world_3.log
V		{example_pipelines/hello_world ← SIS/test_runner_script}/hello_world.yaml
A		example_pipelines/hello_world/hello_world_input.tar
V	(dir)	{example_pipelines/hello_world/pipeline/ ← SIS/hello_world_pipeline/pipeline}
V		{example_pipelines/hello_world ← SIS/hello_world_pipeline}/pipeline/hello_world_pipeline.snake
D		sciCORE
D		sciCORE/pipeline1
D		sciCORE/pipeline1/README.txt
D		sciCORE/pipeline1/Singularity
D		sciCORE/pipeline1/slurm-submit-script-WITH-containers.sh
D		sciCORE/pipeline1/slurm-submit-script-WITHOUT-containers.sh
V	(dir)	{sciCORE/pipeline2/ → example_pipelines/bioinformatics_pipeline2}
V		{sciCORE/pipeline2 → example_pipelines/bioinformatics_pipeline2}/README.txt
V		{sciCORE/pipeline2 → example_pipelines/bioinformatics_pipeline2}/Singularity
V		{sciCORE/pipeline2 → example_pipelines/bioinformatics_pipeline2}/slurm-submit-script-WITH-containers.sh
V		{sciCORE/pipeline2 → example_pipelines/bioinformatics_pipeline2}/slurm-submit-script-WITHOUT-containers.sh
A	(dir)	singularity-pipeline-runner/
V		{singularity-pipeline-runner ← SIS/test_runner_script}/.gitignore
V		{singularity-pipeline-runner ← UniBe}/README.md
V		{singularity-pipeline-runner/bioinformatics_pipeline2.singularity ← SIS/scicore_pipeline2_LSF/Singularity}
V		{singularity-pipeline-runner/bioinformatics_pipeline2.yaml ← UniBe/scicore-pipeline-2a.yaml}
V		{singularity-pipeline-runner ← SIS/test_runner_script}/cowsay.yaml
V		{singularity-pipeline-runner/hello_world.yaml ← UniBe/pipeline.yaml}
V		{singularity-pipeline-runner ← UniBe}/pipeline.py
V		{singularity-pipeline-runner ← UniBe}/requirements.txt
V		{singularity-pipeline-runner ← UniBe}/slurm-submit-script-WITH-containers.sh