92 lines
1.8 KiB
Nix
92 lines
1.8 KiB
Nix
{ lib
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, fetchFromGitHub
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, python3
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, rsync
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}:
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python3.pkgs.buildPythonApplication rec {
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pname = "toil";
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version = "5.7.1";
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format = "setuptools";
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src = fetchFromGitHub {
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owner = "DataBiosphere";
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repo = pname;
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rev = "refs/tags/releases/${version}";
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hash = "sha256-m+XvNyzd0ly2YqKhgxezgGaCXLs3CmupJMnp5RIZqNI=";
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};
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postPatch = ''
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substituteInPlace requirements.txt \
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--replace "docker>=3.7.2, <6" "docker"
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'';
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propagatedBuildInputs = with python3.pkgs; [
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addict
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dill
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docker
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enlighten
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psutil
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py-tes
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pypubsub
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python-dateutil
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pytz
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pyyaml
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requests
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typing-extensions
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];
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checkInputs = [
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rsync
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] ++ (with python3.pkgs; [
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boto
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botocore
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flask
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mypy-boto3-s3
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pytestCheckHook
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stubserver
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]);
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pytestFlagsArray = [
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"src/toil/test"
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];
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pythonImportsCheck = [
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"toil"
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];
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disabledTestPaths = [
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# Tests are reaching their timeout
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"src/toil/test/docs/scriptsTest.py"
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"src/toil/test/jobStores/jobStoreTest.py"
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"src/toil/test/provisioners/aws/awsProvisionerTest.py"
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"src/toil/test/src"
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"src/toil/test/wdl"
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"src/toil/test/utils/utilsTest.py"
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];
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disabledTests = [
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# Tests fail starting with 5.7.1
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"testServices"
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"testConcurrencyWithDisk"
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"testJobConcurrency"
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"testNestedResourcesDoNotBlock"
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"test_omp_threads"
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"testFileSingle"
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"testFileSingle10000"
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"testFileSingleCheckpoints"
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"testFileSingleNonCaching"
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"testFetchJobStoreFiles"
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"testFetchJobStoreFilesWSymlinks"
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"testJobStoreContents"
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"test_cwl_on_arm"
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"test_cwl_toil_kill"
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];
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meta = with lib; {
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description = "Workflow engine written in pure Python";
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homepage = "https://toil.ucsc-cgl.org/";
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license = with licenses; [ asl20 ];
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maintainers = with maintainers; [ veprbl ];
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};
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}
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