diff --git a/planemo_ci_actions.sh b/planemo_ci_actions.sh index 8adec31..a805bd5 100755 --- a/planemo_ci_actions.sh +++ b/planemo_ci_actions.sh @@ -1,14 +1,6 @@ #!/usr/bin/env bash set -exo pipefail -# function running an infinite loop pruning (unused) docker images -function background_prune_docker { - while true; do - docker system prune --all --volumes --force &> /dev/null - sleep 60 - done -} - PLANEMO_TEST_OPTIONS=("--database_connection" "$DATABASE_CONNECTION" "--galaxy_source" "https://github.com/$GALAXY_FORK/galaxy" "--galaxy_branch" "$GALAXY_BRANCH" "--galaxy_python_version" "$PYTHON_VERSION" --test_timeout "$TEST_TIMEOUT") PLANEMO_CONTAINER_DEPENDENCIES=("--biocontainers" "--no_dependency_resolution" "--no_conda_auto_init" "--docker_extra_volume" "./") PLANEMO_WORKFLOW_OPTIONS=("--tool_data_table" "/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml" "--tool_data_table" "/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml" "--docker_extra_volume" "/cvmfs" --shed_tool_conf /tmp/shed_tool_conf.xml --shed_tool_path /tmp/shed_dir) @@ -160,14 +152,12 @@ if [ "$MODE" == "test" ]; then # show tools cat tool_list_chunk.txt - - background_prune_docker & - PRUNE_PID=$! - + # Test tools mkdir -p json_output touch .tt_biocontainer_skip while read -r -a TOOL_GROUP; do + docker system prune --all --force --volumes || true # Check if any of the lines in .tt_biocontainer_skip is a substring of $TOOL_GROUP if echo "${TOOL_GROUP[@]}" | grep -qf .tt_biocontainer_skip; then PLANEMO_OPTIONS=() @@ -189,8 +179,6 @@ if [ "$MODE" == "test" ]; then planemo test_reports tool_test_output.json --test_output tool_test_output.html mv tool_test_output.json tool_test_output.html upload/ - - kill "$PRUNE_PID" fi # combine reports mode