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adjustment for docker build
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build-cwltool-docker.sh

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@@ -7,7 +7,7 @@ docker run -it -v /var/run/docker.sock:/var/run/docker.sock \
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-v /tmp:/tmp \
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-v "$PWD":/tmp/cwltool \
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quay.io/commonwl/cwltool_module /bin/sh -c \
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"apk add gcc bash && pip install -r/tmp/cwltool/test-requirements.txt ; pytest -k 'not (test_bioconda or test_double_overwrite or test_env_filtering or test_biocontainers or test_disable_file_overwrite_without_ext or test_disable_file_creation_in_outdir_with_ext or test_write_write_conflict or test_directory_literal_with_real_inputs_inside or test_revsort_workflow)' --ignore-glob '*test_udocker.py' -n auto -v -rs --pyargs cwltool"
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"apk add gcc bash && pip install -r/tmp/cwltool/test-requirements.txt ; pytest -k 'not (test_bioconda or test_double_overwrite or test_env_filtering or test_biocontainers or test_disable_file_overwrite_without_ext or test_disable_file_creation_in_outdir_with_ext or test_write_write_conflict or test_directory_literal_with_real_inputs_inside or test_revsort_workflow or test_stdin_with_id_preset)' --ignore-glob '*test_udocker.py' -n auto -v -rs --pyargs cwltool"
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version=$(git describe --tags)
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if echo "$version" | grep -vq '\-' >& /dev/null ; then

cwltool.Dockerfile

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@@ -14,7 +14,6 @@ RUN rm /wheels/schema_salad*
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RUN pip install black
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RUN SCHEMA_SALAD_USE_MYPYC=1 MYPYPATH=typeshed pip wheel --no-binary schema-salad \
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$(grep schema.salad requirements.txt) black --wheel-dir=/wheels
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RUN rm /wheels/pyparsing-3*
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RUN pip install --force-reinstall --no-index --no-warn-script-location --root=/pythonroot/ /wheels/*.whl
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# --force-reinstall to install our new mypyc compiled schema-salad package
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