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fix wrong variable name #3253

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merged 2 commits into from
Oct 16, 2020
Merged

fix wrong variable name #3253

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ffd2df1
fix wrong variable name
bernt-matthias Oct 16, 2020
366824d
dont grep with -l
bernt-matthias Oct 16, 2020
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -87,13 +87,13 @@ jobs:
run: |
mkdir json_output/
while read -r TOOLS; do
if grep -lqf .tt_biocontainer_skip <(echo $DIR); then
if grep -lqf .tt_biocontainer_skip <(echo $TOOLS); then
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PLANEMO_OPTIONS=""
else
PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
fi
json=$(mktemp -u -p json_output --suff .json)
PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy --no_conda_auto_init --galaxy_branch $GALAXY_RELEASE --biocontainers --no_dependency_resolution --galaxy_python_version ${{ matrix.python-version }} --test_output_json $json $TOOLS || true
PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json $json $TOOLS || true
docker system prune --all --force --volumes || true
done < tool.list
- name: Merge tool_test_output.json files
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