def install_tool(context,galaxy,toolshed,owner,repository, revision,tool_panel_section,timeout,no_wait): """ Install tool from toolshed. Installs the specified tool from REPOSITORY owned by OWNER in TOOLSHED, into GALAXY. Optionally also specify a changeset REVISION; if no revision is specified and no version of the tool is already installed then will attempt to install the latest revision (otherwise will skip installation). Installation will fail if the specified revision is not installable, or if no installable revisions are found. """ # Get a Galaxy instance gi = context.galaxy_instance(galaxy) if gi is None: logger.critical("Failed to connect to Galaxy instance") return 1 # Install tool return tools.install_tool( gi,toolshed,repository,owner,revision=revision, tool_panel_section=tool_panel_section, timeout=timeout,no_wait=no_wait)
def install_repositories(context,galaxy,file,timeout,no_wait): """ Install tool repositories listed in a file. Installs the tools specified in FILE into GALAXY. FILE should be a tab-delimited file with the columns: TOOLSHED|OWNER|REPOSITORY|REVISON|SECTION If the REVISION field is blank then nebulizer will attempt to install the latest revision; if the SECTION field is blank then the tool will be installed at the top level of the tool panel (i.e. not in any section). """ # Get a Galaxy instance gi = context.galaxy_instance(galaxy) if gi is None: logger.critical("Failed to connect to Galaxy instance") return 1 # Keep a list of failed tool installs failed_install = [] # Install tools for line in file: if line.startswith('#'): continue print line.rstrip('\n') line = line.rstrip('\n').split('\t') try: toolshed,owner,repository = line[:3] except ValueError: logger.critical("Couldn't parse line") return 1 try: revision = line[3] if not revision: revision = None except KeyError: revision = None try: tool_panel_section = line[4] if not tool_panel_section: tool_panel_section = None except KeyError: tool_panel_section = None status = tools.install_tool(gi, toolshed,repository,owner, revision=revision, tool_panel_section=tool_panel_section, timeout=timeout,no_wait=no_wait) if status != tools.TOOL_INSTALL_OK: failed_install.append(line) # List any failed tool installations if failed_install: logger.error("Some requested tool repositories couldn't be " "installed") for repo in failed_install: click.echo('\t'.join(repo)) return 1 # Looks like everything worked return 0
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)