if len(out) == 0 : out = default return out if __name__ == '__main__' : TERM_ESCAPE = True try : pipeline_args = {} # herro announce('ChIPSeq Experiment Pipeline Script Generator') print textwrap.fill(start_text) opts, args = parser.parse_args(sys.argv[1:]) if len(args) > 0 : warn("Arguments were passed, but this script doesn't accept any arguments, rudely ignoring them...\n") # this dictionary will be used to generate a JSON formatted file with # all the relevant settings for the pipeline json_dict = {} ############################################################################ # name of the experiment ############################################################################ def_path = os.path.basename(os.getcwd()) exp_name = input('Experiment name',def_path)
if len(out) == 0 : out = default return out if __name__ == '__main__' : TERM_ESCAPE = True try : pipeline_args = [] # list of (arg_key,arg_val) tuples # herro announce('ChIP-Seq Experiment Read Alignment Pipeline Script Generator') print textwrap.fill(start_text) opts, args = parser.parse_args(sys.argv[1:]) if len(args) > 0 : warn("Arguments were passed, but this script doesn't accept any arguments, rudely ignoring them...\n") # this dictionary will be used to generate a JSON formatted file with # all the relevant settings for the pipeline json_dict = {} modules_list = [] ############################################################################ # get settings ############################################################################ global_tool_settings = get_global_tool_settings()
if len(out) == 0 : out = default return out if __name__ == '__main__' : TERM_ESCAPE = True try : pipeline_args = {} # herro announce('ChIPSeq Experiment Pipeline Script Generator, v0.6') print textwrap.fill(start_text) opts, args = parser.parse_args(sys.argv[1:]) if len(args) > 0 : warn("Arguments were passed, but this script doesn't accept any arguments, rudely ignoring them...\n") # this dictionary will be used to generate a JSON formatted file with # all the relevant settings for the pipeline json_dict = {} ############################################################################ # get settings ############################################################################ global_tool_settings = get_global_tool_settings() local_tool_settings = get_local_tool_settings()