comparison autogenJB2.py @ 66:bc10ad1dfb98 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty

65:c81902830900

from jbrowse2 import JbrowseConnector as jbC

logging.basicConfig(level=logging.debug)
log = logging.getLogger("jbrowse")


def makeDefaultLocation():

    refName = jc.genome_firstcontig
    defloc = "%s:100..10000" % refName
    return defloc


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")

            # "secondary_color": root.find("metadata/general/secondary_color").text,
            # "tertiary_color": root.find("metadata/general/tertiary_color").text,
            # "quaternary_color": root.find("metadata/general/quaternary_color").text,
            # "font_size": root.find("metadata/general/font_size").text,
            # }
            # jc.add_general_configuration(general_data)
            trackconf = jc.config_json.get("tracks", [])
            for gnome in jc.genome_names:
                trackconf += jc.tracksToAdd[gnome]
            jc.config_json["tracks"] = trackconf
            jc.write_config()
            defLoc = makeDefaultLocation()
            default_session_data.update(
                {"defaultLocation": defLoc, "session_name": sessName}
            )
            track_conf.update(default_session_data)
            jc.add_default_session(default_session_data)
            # jc.text_index() not sure what broke here.
    else:
        sys.stderr.write(
            "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
        )

66:bc10ad1dfb98

from jbrowse2 import JbrowseConnector as jbC

logging.basicConfig(level=logging.debug)
log = logging.getLogger("jbrowse")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")

            # "secondary_color": root.find("metadata/general/secondary_color").text,
            # "tertiary_color": root.find("metadata/general/tertiary_color").text,
            # "quaternary_color": root.find("metadata/general/quaternary_color").text,
            # "font_size": root.find("metadata/general/font_size").text,
            # }
            jc.add_general_configuration({})
            trackconf = jc.config_json.get("tracks", [])
            for gnome in jc.genome_names:
                trackconf += jc.tracksToAdd[gnome]
            jc.config_json["tracks"] = trackconf
            jc.write_config()
            default_session_data.update(
                {"session_name": sessName}
            )
            track_conf.update(default_session_data)
            jc.add_default_session(default_session_data)
            # jc.text_index() not sure what broke here.
    else:
        sys.stderr.write(
            "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
        )