diff --git a/local_env.sh.sample b/local_env.sh.sample
index 6eb9b4085b2e921917a7a18ed0ba5d9f521ea84c..4a27ee33ad0e9cb23371e5f90a5afb38cb3275cc 100644
--- a/local_env.sh.sample
+++ b/local_env.sh.sample
@@ -7,7 +7,11 @@
 
 ## If you wish to use a variety of Galaxy tools that depend on galaxy.eggs being defined, 
 ## set GALAXY_HOME to point to a copy of Galaxy.
-#export GALAXY_HOME=/path/to/galaxy-dist
+#export GALAXY_HOME=/path/to/galaxy
+
+## In order to set metadata on the pulsar side, Pulsar needs to know where
+## Galaxy's virtualenv is. If not using remote metadata, this is unnecessary.
+#export GALAXY_VIRTUAL_ENV=/path/to/galaxy/.venv
 
 ## Uncomment to verify GALAXY_HOME is set properly before starting the Pulsar.
 #export TEST_GALAXY_LIBS=1
diff --git a/pulsar/client/client.py b/pulsar/client/client.py
index e3af9783fd475c78eb42362bad96cad93af8a52b..ae6f24d280fd1be0ad34e6c65fc797d15867d516 100644
--- a/pulsar/client/client.py
+++ b/pulsar/client/client.py
@@ -63,7 +63,7 @@ class BaseJobClient(object):
 
         self.setup_handler = build_setup_handler(self, destination_params)
 
-    def setup(self, tool_id=None, tool_version=None):
+    def setup(self, tool_id=None, tool_version=None, preserve_galaxy_python_environment=None):
         """
         Setup remote Pulsar server to run this job.
         """
@@ -72,6 +72,8 @@ class BaseJobClient(object):
             setup_args["tool_id"] = tool_id
         if tool_version:
             setup_args["tool_version"] = tool_version
+        if preserve_galaxy_python_environment:
+            setup_args["preserve_galaxy_python_environment"] = preserve_galaxy_python_environment
         return self.setup_handler.setup(**setup_args)
 
     @property
@@ -394,9 +396,11 @@ def _setup_params_from_job_config(job_config):
     job_id = job_config.get("job_id", None)
     tool_id = job_config.get("tool_id", None)
     tool_version = job_config.get("tool_version", None)
+    preserve_galaxy_python_environment = job_config.get("preserve_galaxy_python_environment", None)
     return dict(
         job_id=job_id,
         tool_id=tool_id,
         tool_version=tool_version,
         use_metadata=True,
+        preserve_galaxy_python_environment=preserve_galaxy_python_environment,
     )
diff --git a/pulsar/client/setup_handler.py b/pulsar/client/setup_handler.py
index 8147579499c37cfb22d0d9692131959c3ef0a350..e0fe6f9398f3d9a3bfbf05cd415eefec42b4fab9 100644
--- a/pulsar/client/setup_handler.py
+++ b/pulsar/client/setup_handler.py
@@ -39,13 +39,14 @@ class LocalSetupHandler(object):
         self.system_properties = system_properties
         self.jobs_directory = destination_args["jobs_directory"]
 
-    def setup(self, job_id, tool_id=None, tool_version=None):
+    def setup(self, job_id, tool_id=None, tool_version=None, preserve_galaxy_python_environment=None):
         return build_job_config(
             job_id=job_id,
             job_directory=self.client.job_directory,
             system_properties=self.system_properties,
             tool_id=tool_id,
             tool_version=tool_version,
+            preserve_galaxy_python_environment=preserve_galaxy_python_environment,
         )
 
     @property
@@ -75,7 +76,7 @@ class RemoteSetupHandler(object):
         return False
 
 
-def build_job_config(job_id, job_directory, system_properties={}, tool_id=None, tool_version=None):
+def build_job_config(job_id, job_directory, system_properties={}, tool_id=None, tool_version=None, preserve_galaxy_python_environment=None):
     """
     """
     inputs_directory = job_directory.inputs_directory()
@@ -100,6 +101,7 @@ def build_job_config(job_id, job_directory, system_properties={}, tool_id=None,
         "job_id": job_id,
         "system_properties": system_properties,
         "pulsar_version": pulsar_version,
+        "preserve_galaxy_python_environment": preserve_galaxy_python_environment,
     }
     if tool_id:
         job_config["tool_id"] = tool_id
diff --git a/pulsar/manager_endpoint_util.py b/pulsar/manager_endpoint_util.py
index f0baadc759309517394ca93b25ff27052c476eeb..f57163d5047b13cd8a48b16e325134730384aa6e 100644
--- a/pulsar/manager_endpoint_util.py
+++ b/pulsar/manager_endpoint_util.py
@@ -80,7 +80,7 @@ def submit_job(manager, job_config):
             input_job_id,
             tool_id,
             tool_version,
-            use_metadata
+            use_metadata,
         )
 
     if job_config is not None:
@@ -98,6 +98,7 @@ def submit_job(manager, job_config):
         submit_params,
         dependencies_description=dependencies_description,
         env=env,
+        setup_params=setup_params,
     )
 
 
diff --git a/pulsar/managers/__init__.py b/pulsar/managers/__init__.py
index eb088171133525c7ab4cf0f1aa83cde7cf5fca3f..68bdc02b1644cc6b4183d811262f218d2e4cdaa0 100644
--- a/pulsar/managers/__init__.py
+++ b/pulsar/managers/__init__.py
@@ -26,7 +26,7 @@ class ManagerInterface(object):
         """
 
     @abstractmethod
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
         """
         Called to indicate that the client is ready for this job with specified
         job id and command line to be executed (i.e. run or queue this job
diff --git a/pulsar/managers/base/__init__.py b/pulsar/managers/base/__init__.py
index 91d275703d3abaeee8d3cc977d922e84641a2432..bdda6b14895a5b96e2d94c7209c2d31806042397 100644
--- a/pulsar/managers/base/__init__.py
+++ b/pulsar/managers/base/__init__.py
@@ -87,6 +87,7 @@ class BaseManager(ManagerInterface):
 
     def __init_galaxy_system_properties(self, kwds):
         self.galaxy_home = kwds.get('galaxy_home', None)
+        self.galaxy_virtual_env = kwds.get('galaxy_virtual_env', None)
         self.galaxy_config_file = kwds.get('galaxy_config_file', None)
         self.galaxy_dataset_files_path = kwds.get('galaxy_dataset_files_path', None)
         self.galaxy_datatypes_config_file = kwds.get('galaxy_datatypes_config_file', None)
@@ -98,6 +99,9 @@ class BaseManager(ManagerInterface):
         galaxy_home = self._galaxy_home()
         if galaxy_home:
             system_properties["galaxy_home"] = galaxy_home
+        galaxy_virtual_env = self._galaxy_virtual_env()
+        if galaxy_virtual_env:
+            system_properties["galaxy_virtual_env"] = galaxy_virtual_env
         for property in ['galaxy_config_file', 'galaxy_dataset_files_path', 'galaxy_datatypes_config_file']:
             value = getattr(self, property, None)
             if value:
@@ -116,6 +120,9 @@ class BaseManager(ManagerInterface):
     def _galaxy_home(self):
         return self.galaxy_home or getenv('GALAXY_HOME', None)
 
+    def _galaxy_virtual_env(self):
+        return self.galaxy_virtual_env or getenv('GALAXY_VIRTUAL_ENV', None)
+
     def _galaxy_lib(self):
         galaxy_home = self._galaxy_home()
         galaxy_lib = None
diff --git a/pulsar/managers/base/base_drmaa.py b/pulsar/managers/base/base_drmaa.py
index cbd27dcaec873b8336c34779de135d4993711fbe..d81602acbff51a877550d9987b65ba4abde0827a 100644
--- a/pulsar/managers/base/base_drmaa.py
+++ b/pulsar/managers/base/base_drmaa.py
@@ -51,12 +51,18 @@ class BaseDrmaaManager(ExternalBaseManager):
             JobState.FAILED: status.COMPLETE,  # Should be a FAILED state here as well
         }[drmaa_state]
 
-    def _build_template_attributes(self, job_id, command_line, dependencies_description=None, env=[], submit_params={}):
+    def _build_template_attributes(self, job_id, command_line, dependencies_description=None, env=[], submit_params={}, setup_params=None):
         stdout_path = self._stdout_path(job_id)
         stderr_path = self._stderr_path(job_id)
 
         attributes = {
-            "remoteCommand": self._setup_job_file(job_id, command_line, dependencies_description=dependencies_description, env=env),
+            "remoteCommand": self._setup_job_file(
+                job_id,
+                command_line,
+                dependencies_description=dependencies_description,
+                env=env,
+                setup_params=setup_params
+            ),
             "jobName": self._job_name(job_id),
             "outputPath": ":%s" % stdout_path,
             "errorPath": ":%s" % stderr_path,
diff --git a/pulsar/managers/base/directory.py b/pulsar/managers/base/directory.py
index 0463b84c9b0c2ba4de0a091cd2a882418047eece..2bdb52b041ebd5f9fc6cc6af5132577ed1a8514c 100644
--- a/pulsar/managers/base/directory.py
+++ b/pulsar/managers/base/directory.py
@@ -104,20 +104,23 @@ class DirectoryBaseManager(BaseManager):
         return tool_id
 
     # Helpers methods related to setting up job script files.
-    def _setup_job_file(self, job_id, command_line, dependencies_description=None, env=[]):
+    def _setup_job_file(self, job_id, command_line, dependencies_description=None, env=[], setup_params=None):
         command_line = self._expand_command_line(command_line, dependencies_description, job_directory=self.job_directory(job_id).job_directory)
-        script_env = self._job_template_env(job_id, command_line=command_line, env=env)
+        script_env = self._job_template_env(job_id, command_line=command_line, env=env, setup_params=setup_params)
         script = job_script(**script_env)
         return self._write_job_script(job_id, script)
 
-    def _job_template_env(self, job_id, command_line=None, env=[]):
+    def _job_template_env(self, job_id, command_line=None, env=[], setup_params=None):
         return_code_path = self._return_code_path(job_id)
         # TODO: Add option to ignore remote env.
         env = env + self.env_vars
+        setup_params = setup_params or {}
         env_setup_commands = map(env_to_statement, env)
         job_template_env = {
             'job_instrumenter': self.job_metrics.default_job_instrumenter,
+            'galaxy_virtual_env': self._galaxy_virtual_env(),
             'galaxy_lib': self._galaxy_lib(),
+            'preserve_python_environment': setup_params.get('preserve_galaxy_python_environment', False),
             'env_setup_commands': env_setup_commands,
             'exit_code_path': return_code_path,
             'working_directory': self.job_directory(job_id).working_directory(),
diff --git a/pulsar/managers/queued.py b/pulsar/managers/queued.py
index 5295af15f65e06310fd3702eaab8b6c73d840ebb..ac3758272d6bcd7be6dc9355e1e8bd988534417b 100644
--- a/pulsar/managers/queued.py
+++ b/pulsar/managers/queued.py
@@ -45,8 +45,14 @@ class QueueManager(Manager):
             worker.start()
             self.work_threads.append(worker)
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
-        command_line = self._prepare_run(job_id, command_line, dependencies_description=dependencies_description, env=env)
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
+        command_line = self._prepare_run(
+            job_id,
+            command_line,
+            dependencies_description=dependencies_description,
+            env=env,
+            setup_params=setup_params
+        )
         try:
             self._job_directory(job_id).store_metadata(JOB_FILE_COMMAND_LINE, command_line)
         except Exception:
diff --git a/pulsar/managers/queued_cli.py b/pulsar/managers/queued_cli.py
index 016cd6c62e81c99389586854155f4be56c6b84e7..943ee062dc4b3247b45332c2eaff2be6480b5217 100644
--- a/pulsar/managers/queued_cli.py
+++ b/pulsar/managers/queued_cli.py
@@ -20,14 +20,19 @@ class CliQueueManager(ExternalBaseManager):
         self.cli_interface = CliInterface(code_dir='.')
         self.shell_params, self.job_params = split_params(kwds)
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
         self._check_execution_with_tool_file(job_id, command_line)
         shell, job_interface = self.__get_cli_plugins()
         stdout_path = self._stdout_path(job_id)
         stderr_path = self._stderr_path(job_id)
         job_name = self._job_name(job_id)
         command_line = self._expand_command_line(command_line, dependencies_description, job_directory=self.job_directory(job_id).job_directory)
-        job_script_kwargs = self._job_template_env(job_id, command_line=command_line, env=env)
+        job_script_kwargs = self._job_template_env(
+            job_id,
+            command_line=command_line,
+            env=env,
+            setup_params=setup_params
+        )
         extra_kwargs = job_interface.job_script_kwargs(stdout_path, stderr_path, job_name)
         job_script_kwargs.update(extra_kwargs)
         script = job_script(**job_script_kwargs)
diff --git a/pulsar/managers/queued_condor.py b/pulsar/managers/queued_condor.py
index 2baa156e20fbc3014a7184f245f018c607e54491..5fb7140a0189f31fa7b2e7c24d888d6d78b269af 100644
--- a/pulsar/managers/queued_condor.py
+++ b/pulsar/managers/queued_condor.py
@@ -26,9 +26,15 @@ class CondorQueueManager(ExternalBaseManager):
         self.user_log_sizes = {}
         self.state_cache = {}
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
         self._check_execution_with_tool_file(job_id, command_line)
-        job_file_path = self._setup_job_file(job_id, command_line, dependencies_description=dependencies_description, env=env)
+        job_file_path = self._setup_job_file(
+            job_id,
+            command_line,
+            dependencies_description=dependencies_description,
+            env=env,
+            setup_params=setup_params
+        )
         log_path = self.__condor_user_log(job_id)
         open(log_path, 'w')  # Touch log file
         build_submit_params = dict(
diff --git a/pulsar/managers/queued_drmaa.py b/pulsar/managers/queued_drmaa.py
index 0ffc68fd0e61069f1c3c9408677df68de10c5211..d4efb9cc0db96d7f56524cc2e47a0c72d217f854 100644
--- a/pulsar/managers/queued_drmaa.py
+++ b/pulsar/managers/queued_drmaa.py
@@ -10,7 +10,7 @@ class DrmaaQueueManager(BaseDrmaaManager):
     """
     manager_type = "queued_drmaa"
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
         self._check_execution_with_tool_file(job_id, command_line)
         attributes = self._build_template_attributes(
             job_id,
@@ -18,6 +18,7 @@ class DrmaaQueueManager(BaseDrmaaManager):
             dependencies_description=dependencies_description,
             env=env,
             submit_params=submit_params,
+            setup_params=setup_params,
         )
         external_id = self.drmaa_session.run_job(**attributes)
         log.info("Submitted DRMAA job with Pulsar job id %s and external id %s", job_id, external_id)
diff --git a/pulsar/managers/queued_drmaa_xsede.py b/pulsar/managers/queued_drmaa_xsede.py
index aae6d209b80220b8f1b7ef9f9b7c373fa49fab48..7123ff22115b469d632d02b060c562095a92fb98 100644
--- a/pulsar/managers/queued_drmaa_xsede.py
+++ b/pulsar/managers/queued_drmaa_xsede.py
@@ -16,13 +16,14 @@ class XsedeDrmaaQueueManager(DrmaaQueueManager):
     """
     manager_type = "queued_drmaa_xsede"
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
         super(XsedeDrmaaQueueManager, self).launch(
             job_id,
             command_line,
             submit_params=submit_params,
             dependencies_description=dependencies_description,
-            env=env
+            env=env,
+            setup_params=setup_params,
         )
         try:
             check_call([
diff --git a/pulsar/managers/queued_external_drmaa.py b/pulsar/managers/queued_external_drmaa.py
index fa7bbb76649cac1a0469eda29bb880388e6a99f5..9925f13f09d19e499cd1a4ebaef7a16337a4cd83 100644
--- a/pulsar/managers/queued_external_drmaa.py
+++ b/pulsar/managers/queued_external_drmaa.py
@@ -31,7 +31,7 @@ class ExternalDrmaaQueueManager(BaseDrmaaManager):
         self.reclaimed = {}
         self.user_map = {}
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
         self._check_execution_with_tool_file(job_id, command_line)
         attributes = self._build_template_attributes(
             job_id,
@@ -39,6 +39,7 @@ class ExternalDrmaaQueueManager(BaseDrmaaManager):
             dependencies_description=dependencies_description,
             env=env,
             submit_params=submit_params,
+            setup_params=setup_params,
         )
         print(open(attributes['remoteCommand'], 'r').read())
         job_attributes_file = self._write_job_file(job_id, 'jt.json', dumps(attributes))
diff --git a/pulsar/managers/unqueued.py b/pulsar/managers/unqueued.py
index 525215a58391c8881e826d7a5d79302f24343843..422a85d1a0e55ece4760726ccf26c65e8a57ebf1 100644
--- a/pulsar/managers/unqueued.py
+++ b/pulsar/managers/unqueued.py
@@ -142,11 +142,11 @@ class Manager(DirectoryBaseManager):
         else:
             self._monitor_execution(job_id, proc, stdout, stderr)
 
-    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[]):
-        command_line = self._prepare_run(job_id, command_line, dependencies_description=dependencies_description, env=env)
+    def launch(self, job_id, command_line, submit_params={}, dependencies_description=None, env=[], setup_params=None):
+        command_line = self._prepare_run(job_id, command_line, dependencies_description=dependencies_description, env=env, setup_params=setup_params)
         self._run(job_id, command_line)
 
-    def _prepare_run(self, job_id, command_line, dependencies_description, env):
+    def _prepare_run(self, job_id, command_line, dependencies_description, env, setup_params=None):
         self._check_execution_with_tool_file(job_id, command_line)
         self._record_submission(job_id)
         if platform.system().lower() == "windows":
@@ -154,7 +154,13 @@ class Manager(DirectoryBaseManager):
             # process them or at least warn about them being ignored.
             command_line = self._expand_command_line(command_line, dependencies_description, job_directory=self.job_directory(job_id).job_directory)
         else:
-            command_line = self._setup_job_file(job_id, command_line, dependencies_description=dependencies_description, env=env)
+            command_line = self._setup_job_file(
+                job_id,
+                command_line,
+                dependencies_description=dependencies_description,
+                env=env,
+                setup_params=setup_params
+            )
         return command_line
 
 
diff --git a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
index 6b3c283bd2e7f5ab191d712112208551fd93f9db..68da1b3e36284ce963d7a39a01d404c394620af7 100644
--- a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
+++ b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
@@ -1,24 +1,33 @@
 #!$shell
 
 $headers
+
+_galaxy_setup_environment() {
+    local _use_framework_galaxy="$1"
+    if [ "$GALAXY_LIB" != "None" -a "$_use_framework_galaxy" = "True" ]; then
+        if [ -n "$PYTHONPATH" ]; then
+            PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
+        else
+            PYTHONPATH="$GALAXY_LIB"
+        fi
+        export PYTHONPATH
+    fi
+    $env_setup_commands
+    if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" \
+         -a "`command -v python`" != "$GALAXY_VIRTUAL_ENV/bin/python" ]; then
+        . "$GALAXY_VIRTUAL_ENV/bin/activate"
+    fi
+}
+
 $integrity_injection
 $slots_statement
 export GALAXY_SLOTS
-GALAXY_LIB="$galaxy_lib"
-if [ "$GALAXY_LIB" != "None" ]; then
-    if [ -n "$PYTHONPATH" ]; then
-        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
-    else
-        PYTHONPATH="$GALAXY_LIB"
-    fi
-    export PYTHONPATH
-fi
-$env_setup_commands
 GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
-if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \
-     -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then
-    . "$GALAXY_VIRTUAL_ENV/bin/activate"
-fi
+_GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
+PRESERVE_GALAXY_ENVIRONMENT="$preserve_python_environment"
+GALAXY_LIB="$galaxy_lib"
+_galaxy_setup_environment "$PRESERVE_GALAXY_ENVIRONMENT"
+GALAXY_PYTHON=`command -v python`
 $instrument_pre_commands
 cd $working_directory
 $command
diff --git a/pulsar/managers/util/job_script/__init__.py b/pulsar/managers/util/job_script/__init__.py
index a08857c24626087d813a7e51b7ea7d1deed328d6..77af249e5c4817d3b05b9e682beb576eef133584 100644
--- a/pulsar/managers/util/job_script/__init__.py
+++ b/pulsar/managers/util/job_script/__init__.py
@@ -1,10 +1,11 @@
 import os
-from string import Template
 import subprocess
 import time
-from pkg_resources import resource_string
+from string import Template
 
+from pkg_resources import resource_string
 from six import text_type
+
 from galaxy.util import unicodify
 
 DEFAULT_SHELL = '/bin/bash'
@@ -44,6 +45,7 @@ OPTIONAL_TEMPLATE_PARAMS = {
     'instrument_post_commands': '',
     'integrity_injection': INTEGRITY_INJECTION,
     'shell': DEFAULT_SHELL,
+    'preserve_python_environment': True,
 }
 
 
@@ -140,9 +142,9 @@ def _handle_script_integrity(path, config):
         raise Exception("Failed to write job script, could not verify job script integrity.")
 
 
-__all__ = [
+__all__ = (
     'check_script_integrity',
     'job_script',
     'write_script',
     'INTEGRITY_INJECTION',
-]
+)