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prune docker containers (continuously) #37

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merged 4 commits into from
Jul 24, 2023
Merged

prune docker containers (continuously) #37

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5208067
prune docker containers at the start of the loop
bernt-matthias Nov 25, 2022
88ae1d8
implement as infinite loop
bernt-matthias Jul 17, 2023
604a3c5
force and redirect
bernt-matthias Jul 17, 2023
9302ac1
fix
bernt-matthias Jul 17, 2023
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16 changes: 14 additions & 2 deletions planemo_ci_actions.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,14 @@
#!/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 "$TEST_TIMEOUT")
PLANEMO_CONTAINER_DEPENDENCIES=("--biocontainers" "--no_dependency_resolution" "--no_conda_auto_init" "--docker_extra_volume" "./")
PLANEMO_WORKFLOW_OPTIONS=("--tool_data_table" "/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml" "--tool_data_table" "/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml" "--docker_extra_volume" "/cvmfs" --shed_tool_conf /tmp/shed_tool_conf.xml --shed_tool_path /tmp/shed_dir)
Expand Down Expand Up @@ -152,7 +160,10 @@ if [ "$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
Expand All @@ -168,7 +179,6 @@ if [ "$MODE" == "test" ]; then
fi
json=$(mktemp -u -p json_output --suff .json)
PIP_QUIET=1 planemo test "${PLANEMO_OPTIONS[@]}" "${PLANEMO_TEST_OPTIONS[@]}" --test_output_json "$json" "${TOOL_GROUP[@]}" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" || true
docker system prune --all --force --volumes || true
done < tool_list_chunk.txt

if [ ! -s tool_list_chunk.txt ]; then
Expand All @@ -179,6 +189,8 @@ 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
Expand Down