diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 2ed9129816f..1e98a97621e 100644 --- a/config/galaxy.ini.sample +++ b/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 diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index e30e44dac87..216e6f4ef37 100644 --- a/lib/galaxy/config.py +++ b/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 ) ) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 2ab12c03c29..4759fa8f1b4 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/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 ): diff --git a/lib/galaxy/jobs/runners/util/job_script/__init__.py b/lib/galaxy/jobs/runners/util/job_script/__init__.py index 9b3c34ef66e..edd8fb31b9a 100644 --- a/lib/galaxy/jobs/runners/util/job_script/__init__.py +++ b/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')