diff --git a/gga_load_data.py b/gga_load_data.py index cf506c107dc01c46e63064e4f0d8fc80317df6f3..cc73e3e2b6dcc0b24dc46503366a15fde4f0a951 100755 --- a/gga_load_data.py +++ b/gga_load_data.py @@ -87,37 +87,6 @@ class LoadData(speciesData.SpeciesData): get_organism_tool_version = get_organism_tool["version"] delete_organism_tool_version = delete_organism_tool["version"] - # if delete_organism_tool["version"] != "2.3.4+galaxy0": - # toolshed_dict = delete_organism_tool["tool_shed_repository"] - # logging.warning("Changeset for %s is not installed" % toolshed_dict["name"]) - # changeset_revision = "b1aa4f9d82fe" - # name = toolshed_dict["name"] - # owner = toolshed_dict["owner"] - # toolshed = "https://" + toolshed_dict["tool_shed"] - # logging.warning("Installing changeset for %s" % toolshed_dict["name"]) - - # self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner, - # changeset_revision=changeset_revision, - # install_tool_dependencies=True, - # install_repository_dependencies=False, - # install_resolver_dependencies=True) - - - # if get_organism_tool["version"] != "2.3.4+galaxy0": - # toolshed_dict = get_organism_tool["tool_shed_repository"] - # logging.warning("Changeset for %s is not installed" % toolshed_dict["name"]) - # changeset_revision = "831229e6cda2" - # name = toolshed_dict["name"] - # owner = toolshed_dict["owner"] - # toolshed = "https://" + toolshed_dict["tool_shed"] - # logging.warning("Installing changeset for %s" % toolshed_dict["name"]) - - # self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner, - # changeset_revision=changeset_revision, - # install_tool_dependencies=True, - # install_repository_dependencies=False, - # install_resolver_dependencies=True) - logging.debug("Getting 'Homo sapiens' ID in instance's chado database") get_sapiens_id_job = self.instance.tools.run_tool( tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/%s" % get_organism_tool_version,