diff --git a/interaction_experiments/check_galaxy.py b/interaction_experiments/check_galaxy.py index 373fc1b96..e45eb82ef 100644 --- a/interaction_experiments/check_galaxy.py +++ b/interaction_experiments/check_galaxy.py @@ -31,7 +31,6 @@ from rocrate.rocrate import ROCrate -GALAXY_IMG = "bgruening/galaxy-stable:20.09" PLANEMO_ENTITY = "https://w3id.org/ro/terms/test#PlanemoEngine" @@ -67,8 +66,7 @@ def check_workflow(crate, crate_dir): new_workflow_path = def_path.parent / workflow_path.name # Planemo expects the test file in the same dir as the workflow shutil.copy2(workflow_path, new_workflow_path) - cmd = ["planemo", "test", "--engine", "docker_galaxy", - "--docker_galaxy_image", GALAXY_IMG, new_workflow_path] + cmd = ["planemo", "test", "--biocontainers", str(new_workflow_path)] print("Running Planemo (this may take a while)") p = subprocess.run(cmd) p.check_returncode() diff --git a/interaction_experiments/data/crates/ro-crate-cwl-basefreqsum/ro-crate-metadata.json b/interaction_experiments/data/crates/ro-crate-cwl-basefreqsum/ro-crate-metadata.json index 526231164..078707714 100644 --- a/interaction_experiments/data/crates/ro-crate-cwl-basefreqsum/ro-crate-metadata.json +++ b/interaction_experiments/data/crates/ro-crate-cwl-basefreqsum/ro-crate-metadata.json @@ -24,9 +24,14 @@ "about": { "@id": "./" }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.1" - } + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] }, { "@id": "./", @@ -102,7 +107,9 @@ }, { "@id": "README.md", - "@type": "File" + "@type": "File", + "about": "./", + "encodingFormat": "text/markdown" }, { "@id": "#cwl", diff --git a/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json b/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json index 9addc5e18..a930b51de 100644 --- a/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json +++ b/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json @@ -24,9 +24,14 @@ "about": { "@id": "./" }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.1" - } + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] }, { "@id": "./", @@ -82,7 +87,9 @@ }, { "@id": "README.md", - "@type": "File" + "@type": "File", + "about": "./", + "encodingFormat": "text/markdown" }, { "@id": "#galaxy", diff --git a/interaction_experiments/requirements.txt b/interaction_experiments/requirements.txt index 19f47f6cf..9b2f1de9b 100644 --- a/interaction_experiments/requirements.txt +++ b/interaction_experiments/requirements.txt @@ -1,2 +1,2 @@ -planemo==0.74.2 -rocrate~=0.4.0 +planemo~=0.74 +rocrate==0.5.2 diff --git a/interaction_experiments/workflow_examples/galaxy/sort-and-change-case/test_on_docker_galaxy.sh b/interaction_experiments/workflow_examples/galaxy/sort-and-change-case/test_on_docker_galaxy.sh index 7df634b4c..019e4594f 100644 --- a/interaction_experiments/workflow_examples/galaxy/sort-and-change-case/test_on_docker_galaxy.sh +++ b/interaction_experiments/workflow_examples/galaxy/sort-and-change-case/test_on_docker_galaxy.sh @@ -5,14 +5,10 @@ set -euo pipefail this="${BASH_SOURCE-$0}" this_dir=$(cd -P -- "$(dirname -- "${this}")" && pwd -P) -# change these as needed -GALAXY_IMG=bgruening/galaxy-stable:20.05 - pushd "${this_dir}" # looks for sort-and-change-case-test.yml in the same dir as # sort-and-change-case.ga planemo test \ - --engine docker_galaxy \ - --docker_galaxy_image "${GALAXY_IMG}" \ + --biocontainers \ sort-and-change-case.ga popd diff --git a/requirements.txt b/requirements.txt index edcd4c8ad..45fdeb9c9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -31,7 +31,6 @@ PyYAML~=5.4.1 pika~=1.2.0 redis~=3.5.3 requests~=2.26.0 -rocrate~=0.4.0 +rocrate==0.5.2 SQLAlchemy~=1.3.23 wheel~=0.37.0 -