diff --git a/lib/galaxy/webapps/tool_shed/config.py b/lib/galaxy/webapps/tool_shed/config.py
index f34a2e49d87..d43437d336a 100644
--- a/lib/galaxy/webapps/tool_shed/config.py
+++ b/lib/galaxy/webapps/tool_shed/config.py
@@ -65,6 +65,8 @@ class Configuration( object ):
self.tool_dependency_dir = None
self.use_tool_dependencies = False
self.update_integrated_tool_panel = False
+ # Galaxy flavor Docker Image
+ self.enable_galaxy_flavor_docker_image = string_as_bool( kwargs.get( "enable_galaxy_flavor_docker_image", "False" ) )
self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
self.user_activation_on = kwargs.get( 'user_activation_on', None )
self.activation_grace_period = kwargs.get( 'activation_grace_period', None )
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index 912606a256e..f74a723da55 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -55,6 +55,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
datatypes_grid = repository_grids.DatatypesGrid()
deprecated_repositories_i_own_grid = repository_grids.DeprecatedRepositoriesIOwnGrid()
email_alerts_repository_grid = repository_grids.EmailAlertsRepositoryGrid()
+ docker_image_grid = repository_grids.DockerImageGrid()
install_matched_repository_grid = repository_grids.InstallMatchedRepositoryGrid()
matched_repository_grid = repository_grids.MatchedRepositoryGrid()
my_writable_repositories_grid = repository_grids.MyWritableRepositoriesGrid()
@@ -985,6 +986,62 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# Do all we can to eliminate spam.
return trans.show_error_message( "You must be logged in to contact the owner of a repository." )
+ @web.expose
+ def create_galaxy_docker_image( self, trans, **kwd ):
+ message = kwd.get( 'message', '' )
+ status = kwd.get( 'status', 'done' )
+ repository_ids = util.listify( kwd.get( 'id', '' ) )
+ if 'operation' in kwd:
+ if repository_ids:
+ operation = kwd[ 'operation' ].lower()
+ if operation == "include in docker image":
+ repository_tups = []
+ for repository_id in repository_ids:
+ repository = suc.get_repository_by_id( trans.app, repository_id )
+ repository_tups.append( ( str( repository.name ),
+ str( repository.user.username ),
+ str( repository.type ) ) )
+ return trans.fill_template( "/webapps/tool_shed/repository/docker_image_repositories.mako",
+ id=','.join( repository_ids ),
+ repository_tups=repository_tups,
+ message=message,
+ status=status )
+ else:
+ # This can only occur when there is a multi-select grid with check boxes and an operation,
+ # and the user clicked the operation button without checking any of the check boxes.
+ kwd[ 'message' ] = "No items were selected."
+ kwd[ 'status' ] = 'error'
+ elif kwd.get( 'create_docker_image_button', False ):
+ tmp_image_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cdidir" )
+ docker_file_name = 'Dockerfile'
+ docker_file_path = os.path.join( tmp_image_dir, docker_file_name )
+ tool_shed_url = tool_shed_url = web.url_for( '/', qualified=True )
+ repository_string = ''
+ for repository_id in repository_ids:
+ repository = suc.get_repository_by_id( trans.app, repository_id )
+ template = basic_util.SELECTED_REPOSITORIES_TEMPLATE
+ repository_template = \
+ string.Template( template ).safe_substitute( tool_shed_url=tool_shed_url,
+ repository_owner=str( repository.user.username ) ,
+ repository_name=str( repository.name ) )
+ repository_string = '%s\n%s' % ( repository_string, repository_template )
+ template = basic_util.DOCKER_IMAGE_TEMPLATE
+ docker_image_template = \
+ string.Template( template ).safe_substitute( selected_repositories=repository_string )
+ docker_image_string = docker_image_template
+ trans.response.set_content_type( 'application/text/plain' )
+ trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % docker_file_name
+ opened_file = open( docker_file_path, "w" )
+ opened_file.write( docker_image_string )
+ opened_file.close()
+ opened_file = open( docker_file_path, "r" )
+ # Make sure the file is removed from disk after the contents have been downloaded.
+ os.unlink( docker_file_path )
+ docker_file_path, docker_file_name = os.path.split( docker_file_path )
+ basic_util.remove_dir( docker_file_path )
+ return opened_file
+ return self.docker_image_grid( trans, **kwd )
+
@web.expose
def create_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index 9a5296adadc..d057db038ff 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -329,6 +329,26 @@ class RepositoryGrid( grids.Grid ):
.outerjoin( model.Category.table )
+class DockerImageGrid( RepositoryGrid ):
+ columns = [
+ RepositoryGrid.NameColumn( "Name",
+ key="name",
+ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
+ attach_popup=False ),
+ RepositoryGrid.DescriptionColumn( "Synopsis",
+ key="description",
+ attach_popup=False ),
+ RepositoryGrid.UserColumn( "Owner",
+ model_class=model.User,
+ link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
+ attach_popup=False,
+ key="User.username" ),
+ RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
+ ]
+ operations = [ grids.GridOperation( "Include in Docker image", allow_multiple=True ) ]
+ show_item_checkboxes = True
+
+
class EmailAlertsRepositoryGrid( RepositoryGrid ):
columns = [
RepositoryGrid.NameColumn( "Name",
diff --git a/lib/tool_shed/util/basic_util.py b/lib/tool_shed/util/basic_util.py
index 7d606081ecd..58dbb17e564 100644
--- a/lib/tool_shed/util/basic_util.py
+++ b/lib/tool_shed/util/basic_util.py
@@ -20,6 +20,33 @@ NO_OUTPUT_TIMEOUT = 1200.0
MAXDIFFSIZE = 8000
MAX_DISPLAY_SIZE = 32768
+DOCKER_IMAGE_TEMPLATE = '''
+# Galaxy Docker image
+
+FROM bgruening/galaxy-stable
+
+MAINTAINER Bjoern A. Gruning, bjoern.gruening@gmail.com
+
+RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini
+
+WORKDIR /galaxy-central
+
+${selected_repositories}
+
+# Mark one folder as imported from the host.
+VOLUME ["/export/"]
+
+# Expose port 80 to the host
+EXPOSE :80
+
+# Autostart script that is invoked during container start
+CMD ["/usr/bin/startup"]
+'''
+
+SELECTED_REPOSITORIES_TEMPLATE = '''
+RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker'
+'''
+
def evaluate_template( text, install_environment ):
"""
Substitute variables defined in XML blocks from dependencies file. The value of the received
diff --git a/templates/webapps/tool_shed/index.mako b/templates/webapps/tool_shed/index.mako
index 34f6331206a..5826c89acf1 100644
--- a/templates/webapps/tool_shed/index.mako
+++ b/templates/webapps/tool_shed/index.mako
@@ -155,6 +155,11 @@
+ %if trans.app.config.enable_galaxy_flavor_docker_image:
+
+ %endif
%if can_review_repositories:
diff --git a/templates/webapps/tool_shed/repository/docker_image_repositories.mako b/templates/webapps/tool_shed/repository/docker_image_repositories.mako
new file mode 100644
index 00000000000..8606da6c185
--- /dev/null
+++ b/templates/webapps/tool_shed/repository/docker_image_repositories.mako
@@ -0,0 +1,64 @@
+<%namespace file="/message.mako" import="render_msg" />
+
+<%!
+ def inherit(context):
+ if context.get('use_panels'):
+ return '/webapps/tool_shed/base_panels.mako'
+ else:
+ return '/base.mako'
+%>
+
+<%inherit file="${inherit(context)}"/>
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+
+
+%if message:
+ ${render_msg( message, status )}
+%endif
+
+
+
+
diff --git a/tool_shed_wsgi.ini.sample b/tool_shed_wsgi.ini.sample
index 2a22906b139..7db0c615ee4 100644
--- a/tool_shed_wsgi.ini.sample
+++ b/tool_shed_wsgi.ini.sample
@@ -90,6 +90,9 @@ sendmail_path = /usr/sbin/sendmail
# Profiling middleware (cProfile based)
## use_profile = True
+# Enable creation of Galaxy flavor Docker Image
+#enable_galaxy_flavor_docker_image = False
+
# Use the new iframe / javascript based layout
use_new_layout = true