Source code for bioblend.toolshed

"""
A base representation of an instance of Tool Shed
"""
from bioblend.galaxyclient import GalaxyClient
from bioblend.toolshed import categories, repositories, tools


[docs]class ToolShedInstance(GalaxyClient):
[docs] def __init__(self, url, key=None, email=None, password=None, verify=True): """ A base representation of a connection to a ToolShed instance, identified by the ToolShed URL and user credentials. After you have created a ``ToolShedInstance`` object, access various modules via the class fields. For example, to work with repositories and get a list of all public repositories, the following should be done:: from bioblend import toolshed ts = toolshed.ToolShedInstance(url='https://testtoolshed.g2.bx.psu.edu') rl = ts.repositories.get_repositories() tools = ts.tools.search_tools('fastq') :type url: str :param url: A FQDN or IP for a given instance of ToolShed. For example: https://testtoolshed.g2.bx.psu.edu . If a ToolShed instance is served under a prefix (e.g. http://127.0.0.1:8080/toolshed/), supply the entire URL including the prefix (note that the prefix must end with a slash). :type key: str :param key: If required, user's API key for the given instance of ToolShed, obtained from the user preferences. :type email: str :param email: ToolShed e-mail address corresponding to the user. Ignored if key is supplied directly. :type password: str :param password: Password of ToolShed account corresponding to the above e-mail address. Ignored if key is supplied directly. :param verify: Whether to verify the server's TLS certificate :type verify: boolean """ super(ToolShedInstance, self).__init__(url, key, email, password, verify=verify) self.categories = categories.ToolShedCategoryClient(self) self.repositories = repositories.ToolShedRepositoryClient(self) self.tools = tools.ToolShedToolClient(self)