def functionalAnnotSeed(infile, outfile): job_memory = str(PARAMS["Eggnogmapper_memory"]) + "G" job_threads = int(PARAMS["Eggnogmapper_threads"]) #generate call to eggnog-mapper #requires older version of diamond to use the eggnog mapper databases statement = "module load bio/diamond/0.8.22 && " statement += PipelineAnnotate.runEggmapSeed(infile, infile, PARAMS) P.run(statement)
def functionalAnnotSeed(infile, outfile): job_memory = str(PARAMS["Eggnogmapper_memory"]) + "G" job_threads = int(PARAMS["Eggnogmapper_threads"]) #generate call to eggnog-mapper #option to add commands to load specific versions of diamond and python2 etc. if needed if PARAMS["Eggnogmapper_preload"] not in ["", "false"]: statement = "{} &&".format(PARAMS["Eggnogmapper_preload"]) else: statement = "" statement += PipelineAnnotate.runEggmapSeed(infile.replace(".log", ""), infile.replace(".log", ""), PARAMS) statement += ' && echo "Made file {}." > {}'.format( outfile.replace(".log", ""), outfile) P.run(statement)