1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/b84bae3b4bbc/ Changeset: b84bae3b4bbc User: greg Date: 2014-07-02 03:44:49 Summary: Add a very basic framework to the Tool Shed for creating a Galaxy flavor Docker Image that uses Bjoern Gruning's Galaxy Docker project. This is a proof-of-concept that should be enhanced if kept. Affected #: 7 files

diff -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -65,6 +65,8 @@ 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 -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -55,6 +55,7 @@ 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() @@ -986,6 +987,62 @@ 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', '' ) status = kwd.get( 'status', 'done' )

diff -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -329,6 +329,26 @@ .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 -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -20,6 +20,33 @@ 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 -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -155,6 +155,11 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='upload_capsule' )}">Import repository capsule</a></div> + %if trans.app.config.enable_galaxy_flavor_docker_image: + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_galaxy_docker_image' )}">Create Galaxy Docker Image</a> + </div> + %endif %if can_review_repositories: <div class="toolSectionPad"></div><div class="toolSectionTitle"> @@ -216,6 +221,11 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a></div> + %if trans.app.config.enable_galaxy_flavor_docker_image: + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_galaxy_docker_image' )}">Create Galaxy Docker Image</a> + </div> + %endif %endif %endif </div>

diff -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab templates/webapps/tool_shed/repository/docker_image_repositories.mako --- /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> + +<%def name="javascripts()"> + ${parent.javascripts()} +</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormBody"> + <div class="form-row"> + <div class="warningmessage"> + Click the <b>Create Docker Image</b> button below to create a Docker Image that will install the following repositories. + </div> + <div style="clear: both"></div> + </div> + </div> +</div> +<div class="toolForm"> + <div class="toolFormTitle">Repositories for inclusion in Docker Image</div> + <form id="docker_image_form" name="docker_image_form" action="${h.url_for( controller='repository', action='create_galaxy_docker_image' )}" enctype="multipart/form-data" method="post"> + <div class="form-row"> + <input type="hidden" name="id" value="${id}" /> + </div> + <div class="form-row"> + <table class="grid"> + <tr> + <th bgcolor="#D8D8D8">Name</th> + <th bgcolor="#D8D8D8">Owner</th> + <th bgcolor="#D8D8D8">Type</th> + </tr> + %for repository_tup in repository_tups: + <% name, owner, type = repository_tup %> + <tr> + <td>${ name | h }</td> + <td>${ owner | h }</td> + <td>${ type | h }</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" class="primary-button" name="create_docker_image_button" value="Create Docker Image"> + </div> + </form> + </div> +</div>

diff -r 4bcf8ca400aee4f72900de8a375707256f0ae369 -r b84bae3b4bbc69241b85ad4b33741e89083304ab tool_shed_wsgi.ini.sample --- a/tool_shed_wsgi.ini.sample +++ b/tool_shed_wsgi.ini.sample @@ -90,6 +90,9 @@ # 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

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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