Add forgotten file

src/toil/test/batchSystems/test_cactus_integration.py

@@ -0,0 +1,60 @@
+import os
+import uuid
+
+from toil.provisioners import cluster_factory
+from toil.test.provisioners.clusterTest import AbstractClusterTest
+
+
+class CactusIntegrationTest(AbstractClusterTest):
+    """
+    Run the Cactus Integration test on a Kubernetes AWS cluster
+    """
+
+    def __init__(self, methodName):
+        super().__init__(methodName=methodName)
+        self.clusterName = "cactus-test-" + str(uuid.uuid4())
+        self.leaderNodeType = "t2.medium"
+        self.clusterType = "kubernetes"
+
+    def setUp(self):
+        super().setUp()
+        self.jobStore = f"aws:{self.awsRegion()}:cluster-{uuid.uuid4()}"
+
+    def test_cactus_integration(self):
+        # Make a cluster with worker nodes
+        self.createClusterUtil(args=["--nodeTypes=t2.xlarge", "-w=1-3"])
+        print("cluster created")
+        # get the leader so we know the IP address - we don't need to wait since create cluster
+        # already ensures the leader is running
+        self.cluster = cluster_factory(
+            provisioner="aws", zone=self.zone, clusterName=self.clusterName
+        )
+        self.leader = self.cluster.getLeader()
+
+        CACTUS_COMMIT_SHA = os.environ["CACTUS_COMMIT_SHA"] or "f5adf4013326322ae58ef1eccb8409b71d761583"  # default cactus commit
+
+        # command to install and run cactus on the cluster
+        print("running cactus")
+        cactus_command = ("python -m virtualenv --system-site-packages venv && "
+                          ". venv/bin/activate && "
+                          "git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive && "
+                          "cd cactus && "
+                          "git fetch origin && "
+                          f"git checkout {CACTUS_COMMIT_SHA} && "
+                          "git submodule update --init --recursive && "
+                          "pip install --upgrade 'setuptools<66' pip && "
+                          "pip install --upgrade . && "
+                          "pip install --upgrade numpy psutil && "
+                          "time cactus --setEnv SINGULARITY_DOCKER_HUB_MIRROR --batchSystem kubernetes --retryCount=3 "
+                          f"--consCores 2 --binariesMode singularity --clean always {self.jobStore} "
+                          "examples/evolverMammals.txt examples/evolverMammals.hal --root mr --defaultDisk 8G --logDebug")
+
+        # run cactus
+        self.sshUtil(
+            [
+                "bash",
+                "-c",
+                cactus_command
+            ]
+        )
+