diff --git a/common b/common index 1660eef..4343111 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 1660eef0b1172c1059270fff77f9abc0a5fc1ea4 +Subproject commit 4343111a4fd80f3bc6d38ec041131bb33d1bba0f diff --git a/scripts/run_benchmark/run_full_local.sh b/scripts/run_benchmark/run_full_local.sh index 4fc4b48..8c63393 100755 --- a/scripts/run_benchmark/run_full_local.sh +++ b/scripts/run_benchmark/run_full_local.sh @@ -21,6 +21,9 @@ exit 1 set -e +echo "Running benchmark on test data" +echo " Make sure to run 'scripts/project/build_all_docker_containers.sh'!" + # generate a unique id RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" publish_dir="resources/results/${RUN_ID}" @@ -40,5 +43,5 @@ nextflow run openproblems-bio/task_template \ -profile docker \ -resume \ -entry auto \ - -c common/nextflow_helpers/labels.config \ + -c common/nextflow_helpers/labels_ci.config \ -params-file /tmp/params.yaml diff --git a/scripts/run_benchmark/run_test_local.sh b/scripts/run_benchmark/run_test_local.sh index 097a949..e549635 100755 --- a/scripts/run_benchmark/run_test_local.sh +++ b/scripts/run_benchmark/run_test_local.sh @@ -16,12 +16,19 @@ exit 1 set -e +echo "Running benchmark on test data" +echo " Make sure to run 'scripts/project/build_all_docker_containers.sh'!" + +# generate a unique id +RUN_ID="testrun_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="resources/results/${RUN_ID}" + # write the parameters to file -cat > /tmp/params.yaml << 'HERE' +cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources_test/task_template/**/state.yaml rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution' output_state: "state.yaml" -publish_dir: s3://openproblems-nextflow/temp/task_template/ +publish_dir: "$publish_dir" HERE nextflow run . \ @@ -29,5 +36,5 @@ nextflow run . \ -profile docker \ -resume \ -entry auto \ - -c common/nextflow_helpers/labels.config \ + -c common/nextflow_helpers/labels_ci.config \ -params-file /tmp/params.yaml