Merge branch 'release_16.01' into dev

create_db.sh

@@ -1,9 +1,11 @@
 #!/bin/sh
 
-if [ -d .venv ];
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
+if [ -d "$GALAXY_VIRTUAL_ENV" ];
 then
-    printf "Activating virtualenv at %s/.venv\n" $(pwd)
-    . .venv/bin/activate
+    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 cd `dirname $0`

lib/galaxy/jobs/__init__.py

@@ -771,6 +771,7 @@ class JobWrapper( object ):
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination( from_job=job )
 
+        self.__commands_in_new_shell = self.app.config.commands_in_new_shell
         self.__user_system_pwent = None
         self.__galaxy_system_pwent = None
 
@@ -803,13 +804,19 @@ class JobWrapper( object ):
     def shell(self):
         return self.job_destination.shell or getattr(self.app.config, 'default_job_shell', DEFAULT_JOB_SHELL)
 
+    def disable_commands_in_new_shell(self):
+        """Provide an extension point to disable this isolation,
+        Pulsar builds its own job script so this is not needed for
+        remote jobs."""
+        self.__commands_in_new_shell = False
+
     @property
     def strict_shell(self):
         return self.tool.strict_shell
 
     @property
     def commands_in_new_shell(self):
-        return self.app.config.commands_in_new_shell
+        return self.__commands_in_new_shell
 
     @property
     def galaxy_lib_dir(self):

lib/galaxy/jobs/runners/pulsar.py

@@ -278,6 +278,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
                 compute_tool_directory=remote_tool_directory,
                 compute_job_directory=remote_job_directory,
             )
+            job_wrapper.disable_commands_in_new_shell()
             command_line = build_command(
                 self,
                 job_wrapper=job_wrapper,

manage_db.sh

@@ -5,10 +5,12 @@
 # sh manage_db.sh downgrade --version=3 <tool_shed if using that webapp - galaxy is the default>
 #######
 
-if [ -d .venv ];
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
+if [ -d "$GALAXY_VIRTUAL_ENV" ];
 then
-    printf "Activating virtualenv at %s/.venv\n" $(pwd)
-    . .venv/bin/activate
+    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 cd `dirname $0`

templates/webapps/galaxy/workflow/run.mako

@@ -388,16 +388,23 @@ from galaxy.jobs.actions.post import ActionBox
 import re
 import colorsys
 import random
+from six import string_types
+
+def get_wf_parms(v, wf_parms):
+    if isinstance(v, dict):
+        [ get_wf_parms(value, wf_parms) for value in v.values()  ]
+    elif isinstance(v, string_types):
+        for rematch in re.findall('\$\{.+?\}', v):
+            if rematch[2:-1] not in wf_parms:
+                wf_parms[rematch[2:-1]] = ""
 
 used_accumulator = []
-
 wf_parms = {}
+
 for step in steps:
     for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
-        if isinstance(v, basestring):
-            for rematch in re.findall('\$\{.+?\}', v):
-                if rematch[2:-1] not in wf_parms:
-                    wf_parms[rematch[2:-1]] = ""
+        get_wf_parms(v, wf_parms)
+
 if wf_parms:
     hue_offset = 1.0 / len(wf_parms)
     hue = 0.0

test/unit/jobs/test_job_wrapper.py

@@ -12,9 +12,6 @@ from galaxy.util.bunch import Bunch
 from galaxy.tools import evaluation
 
 from tools_support import UsesApp
-# from tools_support import MockTool
-
-# from ..tools_and_jobs_helpers import MockApp
 
 TEST_TOOL_ID = "cufftest"
 TEST_VERSION_COMMAND = "bwa --version"
@@ -123,26 +120,6 @@ class MockJobDispatcher(object):
         pass
 
 
-class MockApp(object):
-
-    def __init__(self, object_store, test_directory, model_objects):
-        self.object_store = object_store
-        self.toolbox = MockToolbox(MockTool(self))
-        self.config = Bunch(
-            outputs_to_working_directory=False,
-            new_file_path=os.path.join(test_directory, "new_files"),
-            tool_data_path=os.path.join(test_directory, "tools"),
-            root=os.path.join(test_directory, "galaxy"),
-            datatypes_registry=Bunch(
-                integrated_datatypes_configs=os.path.join(test_directory, "datatypes_conf.xml"),
-            ),
-        )
-        self.job_config = Bunch(
-            dynamic_params=None,
-        )
-        self.model = Bunch(context=MockContext(model_objects))
-
-
 class MockContext(object):
 
     def __init__(self, model_objects):

test/unit/tools_support.py

@@ -111,6 +111,7 @@ class MockApp( object ):
 
         self.config = Bunch(
             outputs_to_working_directory=False,
+            commands_in_new_shell=True,
             new_file_path=os.path.join(test_directory, "new_files"),
             tool_data_path=os.path.join(test_directory, "tools"),
             root=os.path.join(test_directory, "galaxy"),