include: "config" def prepare_environment(stepname): """ Prepare the output directories and logs. stepname: the name of the pipeline step return: the step master directory, the step log """ out = os.path.join(OUTPUTDIR, stepname) # mkdirs if not os.path.exists(out): os.makedirs(out) elif not os.path.isdir(out): raise OSError("//[IMP] Output is not a directory: %s" % out) if not os.path.exists(TMPDIR): os.makedirs(TMPDIR) bench = os.path.join(out, 'benchmarks') if not os.path.exists(bench): os.makedirs(bench) return out, os.path.join(out, '%s.log' % stepname) # INCLUDES PROCESSING RULES include: "rules/Util.rules" include: "rules/Preprocessing/master.rules" include: "rules/Assembly/master.rules" include: "rules/Analysis/master.rules" rule ALL: input: preprocessing_output_files(), assembly_output_files(), analysis_output_files() shell: "echo 'DONE'"