Add Deca (resolves #108)

src/toil_lib/tools/spark_tools.py

@@ -191,3 +191,49 @@ def call_adam(job, master_ip, arguments,
                    default_params +
                    arguments)
 
+def call_deca(job, master_ip, arguments,
+              memory=None,
+              override_parameters=None,
+              run_local=False):
+    """
+    Invokes the DECA container. Find DECA at https://github.com/bigdatagenomics/deca.
+
+    :param toil.Job.job job: The Toil Job calling this function
+    :param masterIP: The Spark leader IP address.
+    :param arguments: Arguments to pass to ADAM.
+    :param memory: Gigabytes of memory to provision for Spark driver/worker.
+    :param override_parameters: Parameters passed by the user, that override our defaults.
+    :param run_local: If true, runs Spark with the --master local[*] setting, which uses
+      all cores on the local machine. The master_ip will be disregarded.
+
+    :type masterIP: MasterAddress
+    :type arguments: list of string
+    :type memory: int or None
+    :type override_parameters: list of string or None
+    :type native_adam_path: string or None
+    :type run_local: boolean
+    """
+    if run_local:
+        master = ["--master", "local[*]"]
+    else:
+        master = ["--master",
+                  ("spark://%s:%s" % (master_ip, SPARK_MASTER_PORT)),
+                  "--conf", ("spark.hadoop.fs.default.name=hdfs://%s:%s" % (master_ip, HDFS_MASTER_PORT)),]
+
+    default_params = (master + [
+            # set max result size to unlimited, see #177
+            "--conf", "spark.driver.maxResultSize=0"])
+
+    docker_parameters = []
+    if master_ip:
+        docker_parameters = master_ip.docker_parameters(["--net=host"])
+    docker_parameters.extend(['--log-driver', 'none'])
+    dockerCall(job=job,
+               tool="quay.io/ucsc_cgl/deca",
+               dockerParameters=docker_parameters,
+               parameters=_make_parameters(master_ip,
+                                           default_params,
+                                           memory,
+                                           arguments,
+                                           override_parameters))
+