#########################
##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
