def update_tool(context,galaxy,toolshed,owner,repository):
"""
Update tool installed from toolshed.
Updates the specified tool from REPOSITORY owned by
OWNER in TOOLSHED, to the latest revision in GALAXY.
The tool must already be present in GALAXY and a newer
changeset revision must be available. The update will
be installed into the same tool panel section as the
original tool.
"""
# 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.update_tool(gi,toolshed,repository,owner,
timeout=timeout,no_wait=no_wait)
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)