90 lines
1.9 KiB
Nix
90 lines
1.9 KiB
Nix
{ lib
|
|
, fetchFromGitHub
|
|
, python3
|
|
, rsync
|
|
}:
|
|
|
|
python3.pkgs.buildPythonApplication rec {
|
|
pname = "toil";
|
|
version = "5.12.0";
|
|
format = "setuptools";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "DataBiosphere";
|
|
repo = pname;
|
|
rev = "refs/tags/releases/${version}";
|
|
hash = "sha256-cTpbQo9tPZifUO59vbnIa3XUinFJ2/5Slfe4yszglFM=";
|
|
};
|
|
|
|
propagatedBuildInputs = with python3.pkgs; [
|
|
addict
|
|
dill
|
|
docker
|
|
enlighten
|
|
psutil
|
|
py-tes
|
|
pypubsub
|
|
python-dateutil
|
|
pytz
|
|
pyyaml
|
|
requests
|
|
typing-extensions
|
|
];
|
|
|
|
nativeCheckInputs = [
|
|
rsync
|
|
] ++ (with python3.pkgs; [
|
|
boto
|
|
botocore
|
|
flask
|
|
pytestCheckHook
|
|
stubserver
|
|
]);
|
|
|
|
pytestFlagsArray = [
|
|
"src/toil/test"
|
|
];
|
|
|
|
pythonImportsCheck = [
|
|
"toil"
|
|
];
|
|
|
|
disabledTestPaths = [
|
|
# Tests are reaching their timeout
|
|
"src/toil/test/docs/scriptsTest.py"
|
|
"src/toil/test/jobStores/jobStoreTest.py"
|
|
"src/toil/test/provisioners/aws/awsProvisionerTest.py"
|
|
"src/toil/test/src"
|
|
"src/toil/test/wdl"
|
|
"src/toil/test/utils/utilsTest.py"
|
|
"src/toil/test/cwl/cwlTest.py"
|
|
"src/toil/test/lib/test_ec2.py"
|
|
"src/toil/test/lib/aws/test_iam.py"
|
|
"src/toil/test/lib/aws/test_s3.py"
|
|
];
|
|
|
|
disabledTests = [
|
|
# Tests fail starting with 5.7.1
|
|
"testServices"
|
|
"testConcurrencyWithDisk"
|
|
"testJobConcurrency"
|
|
"testNestedResourcesDoNotBlock"
|
|
"test_omp_threads"
|
|
"testFileSingle"
|
|
"testFileSingle10000"
|
|
"testFileSingleCheckpoints"
|
|
"testFileSingleNonCaching"
|
|
"testFetchJobStoreFiles"
|
|
"testFetchJobStoreFilesWSymlinks"
|
|
"testJobStoreContents"
|
|
"test_cwl_on_arm"
|
|
"test_cwl_toil_kill"
|
|
];
|
|
|
|
meta = with lib; {
|
|
description = "Workflow engine written in pure Python";
|
|
homepage = "https://toil.ucsc-cgl.org/";
|
|
license = with licenses; [ asl20 ];
|
|
maintainers = with maintainers; [ veprbl ];
|
|
};
|
|
}
|