######################### ##first imports import os,sys,traceback sys.tracebacklimit = 0 shellv = os.environ["SHELL"] ## Setting up paths INITIAL_SRC = "%s%ssrc"%(sys.path[0], os.sep) ## Hardcode a k-mer size DEFAULT_KMER = "31" ## Hardcode a default taxonomic classification level DEFAULT_TAXA_LEVEL = "class" sys.path.insert(1, INITIAL_SRC) validate_install = 0 if validate_install: import check_install rt = check_install.validate_dir(sys.path[0].strip(),sys.path[0]+os.sep+'required_file_list.txt') if rt == -1: print "MetAMOS not properly installed, please reinstall or contact development team for assistance" sys.exit(1) import utils import workflow utils.configureEnvironment(utils.INITIAL_UTILS) ## The usual library dependencies import string import time import datetime import BaseHTTPServer import getopt import re
if not os.path.exists("KronaTools/taxonomy/taxonomy.tab") or 0: print "KronaTools taxonomy data not found, needed for Postprocess, download now (will take around 20 minutes)?" if silentInstall: dl = 'y' else: dl = raw_input("Enter Y/N: ") if dl == 'y' or dl == 'Y': os.system("cd KronaTools && ./updateTaxonomy.sh") # make sure we have setuptools available sys.path.append(METAMOS_ROOT + os.sep + "Utilities" + os.sep + "python") from get_setuptools import use_setuptools use_setuptools() #os.system(" print "Run setup.py.." os.system("python setup.py install_scripts --install-dir=`pwd` build_ext") #print "Compile & optimize" #distutils.util.byte_compile(['./runPipeline.py'],optimize=2,force=True) #os.system("chmod a+wrx runPipeline.pyo") os.system("mv runPipeline.py runPipeline") os.system("mv initPipeline.py initPipeline") validate_install = 1 if validate_install: rt = check_install.validate_dir(METAMOS_ROOT,'required_file_list.txt') if rt == -1: print "MetAMOS not properly installed, please reinstall or contact development team for assistance" sys.exit(1)
######################### ##first imports import os, sys, traceback sys.tracebacklimit = 0 shellv = os.environ["SHELL"] ## Setting up paths INITIAL_SRC = "%s%ssrc" % (sys.path[0], os.sep) ## Hardcode a k-mer size DEFAULT_KMER = "31" ## Hardcode a default taxonomic classification level DEFAULT_TAXA_LEVEL = "class" sys.path.insert(1, INITIAL_SRC) validate_install = 0 if validate_install: import check_install rt = check_install.validate_dir( sys.path[0].strip(), sys.path[0] + os.sep + 'required_file_list.txt') if rt == -1: print "MetAMOS not properly installed, please reinstall or contact development team for assistance" sys.exit(1) import utils import workflow utils.configureEnvironment(utils.INITIAL_UTILS) ## The usual library dependencies import string import time import datetime import BaseHTTPServer import getopt import re