def arg_grab(arg): if arg == "-lapps": return "~/Dropbox/lapps-ansible/tasks/lapps-tools.yml" if arg == "-list": tools.list_tools() exit(0) if arg == "-help": send_help() exit(0) if arg == "lapps_installer.py": return " " else: print "No such toolset ~Sule" exit(0)
def list_tools(context,galaxy,name,installed_only): """ List tools in Galaxy instance. Prints details of tools available in GALAXY instance, including: tool name, version, tool panel section, and toolshed repository and revision changeset. """ # Get a Galaxy instance gi = context.galaxy_instance(galaxy) if gi is None: logger.critical("Failed to connect to Galaxy instance") return 1 # List tools tools.list_tools(gi,name=name,installed_only=installed_only)
def manage_tools(args=None): """ Implements the 'manage_tools' utility """ deprecation_warning() if args is None: args = sys.argv[1:] p = base_parser(usage=\ "\n\t%prog list GALAXY_URL [options]" "\n\t%prog installed GALAXY_URL [options]" "\n\t%prog tool_panel GALAXY_URL [options]" "\n\t%prog install GALAXY_URL [options] SHED OWNER TOOL [REVISION]" "\n\t%prog update GALAXY_URL [options] SHED OWNER TOOL", description="Manage and install tools in a Galaxy " "instance") commands = ['list','installed','tool_panel','install','update'] # Get compulsory arguments if len(args) == 1: if args[0] == '-h' or args[0] == '--help': p.print_usage() elif args[0] == '--version': p.print_version() sys.exit(0) if len(args) < 2: p.error("need to supply a command and a Galaxy URL/alias") command = args[0] galaxy_url = args[1] # Setup additional command line options if command not in commands: p.error("unrecognised command: '%s'" % command) elif command == 'list': p.set_usage("%prog list GALAXY_URL [options]") p.add_option('--name',action='store',dest='name',default=None, help="specific tool name(s) to list") p.add_option('--installed',action='store_true', dest='installed_only',default=False, help="only list tools installed from a toolshed") elif command == 'installed': p.set_usage("%prog installed GALAXY_URL [options]") p.add_option('--name',action='store',dest='name',default=None, help="specific tool repository/ies to list") p.add_option('--toolshed',action='store',dest='toolshed',default=None, help="only list repositories from TOOLSHED") p.add_option('--owner',action='store',dest='owner',default=None, help="only list repositories owned by OWNER") p.add_option('--list-tools',action='store_true',dest='list_tools', default=None, help="list the associated tools for each repository") p.add_option('--updateable',action='store_true',dest='updateable', default=None, help="only show repositories with uninstalled updates " "or upgrades") elif command == 'tool_panel': p.set_usage("%prog tool_panel GALAXY_URL [options]") p.add_option('--name',action='store',dest='name',default=None, help="specific tool panel section(s) to list") p.add_option('--list-tools',action='store_true',dest='list_tools', default=None, help="list the associated tools for each section") elif command == 'install': p.set_usage("%prog install GALAXY_URL [options] SHED OWNER TOOL " "[REVISION]") p.add_option('--tool-panel-section',action='store', dest='tool_panel_section',default=None, help="tool panel section name or id to install the " "tool under") elif command == 'update': p.set_usage("%prog update GALAXY_URL [options] SHED OWNER TOOL") # Process remaining arguments on command line if args[1] in ('-h','--help','--version'): args = args[1:] else: args = args[2:] options,args = p.parse_args(args) handle_debug(debug=options.debug) handle_suppress_warnings(suppress_warnings=options.suppress_warnings) handle_ssl_warnings(verify=(not options.no_verify)) # Handle password if required email,password = handle_credentials(options.username, options.galaxy_password, prompt="Password for %s: " % galaxy_url) # Get a Galaxy instance gi = get_galaxy_instance(galaxy_url,api_key=options.api_key, email=email,password=password, verify_ssl=(not options.no_verify)) if gi is None: logger.critical("Failed to connect to Galaxy instance") sys.exit(1) # Execute command if command == 'list': tools.list_tools(gi,name=options.name, installed_only=options.installed_only) elif command == 'installed': tools.list_installed_repositories(gi,name=options.name, toolshed=options.toolshed, owner=options.owner, list_tools=options.list_tools, only_updateable=options.updateable) elif command == 'tool_panel': tools.list_tool_panel(gi,name=options.name, list_tools=options.list_tools) elif command == 'install': if len(args) < 3: p.error("Need to supply toolshed, owner, repo and optional " "revision") toolshed,owner,repo = args[:3] if len(args) == 4: revision = args[3] else: revision = None status = tools.install_tool( gi,toolshed,repo,owner,revision=revision, tool_panel_section=options.tool_panel_section) sys.exit(status) elif command == 'update': if len(args) != 3: p.error("Need to supply toolshed, owner and repo") toolshed,owner,repo = args[:3] status = tools.update_tool(gi,toolshed,repo,owner) sys.exit(status)