Switch default job shell back to /bin/sh for 16.01.

config/galaxy.ini.sample

@@ -308,11 +308,12 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 
 
 # Set the default shell used by jobs Galaxy-wide. This defaults to
-# bash and can be overidden at the destination level for
+# sh and can be overidden at the destination level for
 # heterogenous clusters. conda job resolution requires bash or zsh
-# so if this is switched to /bin/sh for instance - conda resolution
-# should be disabled.
-#default_job_shell = /bin/bash
+# so if this is not switched to /bin/bash for instance - conda resolution
+# should be disabled. (16.01 will likely be the last release with a
+# default of /bin/sh instead of /bin/bash).
+#default_job_shell = /bin/sh
 
 # Citation related caching.  Tool citations information maybe fetched from
 # external sources such as http://dx.doi.org/ by Galaxy - the following

lib/galaxy/config.py

@@ -169,7 +169,7 @@ class Configuration( object ):
         self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
         self.cluster_files_directory = os.path.abspath( kwargs.get( "cluster_files_directory", "database/pbs" ) )
         self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root )
-        self.default_job_shell = kwargs.get( "default_job_shell", "/bin/bash" )
+        self.default_job_shell = kwargs.get( "default_job_shell", "/bin/sh" )
         self.cleanup_job = kwargs.get( "cleanup_job", "always" )
         self.container_image_cache_path = self.resolve_path( kwargs.get( "container_image_cache_path", "database/container_images" ) )
         self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) )

lib/galaxy/jobs/__init__.py

@@ -44,7 +44,7 @@ log = logging.getLogger( __name__ )
 TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json'
 
 # Override with config.default_job_shell.
-DEFAULT_JOB_SHELL = '/bin/bash'
+DEFAULT_JOB_SHELL = '/bin/sh'
 
 
 class JobDestination( Bunch ):

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -6,7 +6,7 @@ from pkg_resources import resource_string
 
 from galaxy.util import unicodify
 
-DEFAULT_SHELL = '/bin/bash'
+DEFAULT_SHELL = '/bin/sh'
 
 DEFAULT_JOB_FILE_TEMPLATE = Template(
     resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh').decode('UTF-8')