"rm %s/Logs/assemble.ok"%(settings.rundir),\
"RunPipeline")
utils.run_process(settings, \
"rm %s/Assemble/out/*.asm.contig"%(settings.rundir),\
"RunPipeline")
if "Classify" not in skipsteps and "Classify" in forcesteps:
utils.run_process(settings, \
"rm %s/Logs/classify.ok"%(settings.rundir), \
"RunPipeline")
if __name__ == "__main__":
print "Starting metAMOS pipeline"
if settings.threads < 1:
settings.threads = 1
settings = utils.initConfig(settings.kmer, settings.threads, settings.rundir, settings.taxa_level, settings.local_krona, settings.annotate_unmapped, settings.doscaffolding, settings.VERBOSE, settings.OUTPUT_ONLY)
# add krona to system path
currPath = os.environ["PATH"]
if utils.Settings.KRONA not in currPath:
os.environ["PATH"]="%s:%s"%(utils.Settings.KRONA, currPath)
# check for memory/cpu
if not settings.nopsutil and lowmem == False:
import psutil
avram = utils.getAvailableMemory(settings)
print "[Available RAM: %d GB]"%(avram)
lowmem= False
if avram <= 32:
print utils.WARNING_YELLOW+"\tThere is *%d GB of RAM currently available on this machine, suggested minimum of 32 GB"%(avram)+utils.ENDC
print utils.WARNING_YELLOW+"\t*Enabling low MEM mode, might slow down some steps in pipeline"+utils.ENDC
utils.run_process(settings, \
"rm %s/FindORFS/out/%s.fna"%(settings.rundir,settings.PREFIX),"RunPipeline")
utils.run_process(settings, \
"touch %s/Assemble/out/%s.asm.contig"%(settings.rundir,settings.PREFIX),\
"RunPipeline")
if "Assemble" not in skipsteps and "Assemble" in forcesteps:
utils.run_process(settings, \
"rm %s/Logs/assemble.ok"%(settings.rundir),\
"RunPipeline")
if __name__ == "__main__":
print "Starting metAMOS pipeline"
if settings.threads < 1:
settings.threads = 1
settings = utils.initConfig(settings.kmer, settings.threads, settings.rundir, settings.taxa_level, settings.VERBOSE, settings.OUTPUT_ONLY)
# add krona to system path
currPath = os.environ["PATH"]
if utils.Settings.KRONA not in currPath:
os.environ["PATH"]="%s:%s"%(utils.Settings.KRONA, currPath)
# check for memory/cpu
if not nopsutil and lowmem == False:
cacheusage=0
if 'linux' in utils.Settings.OSTYPE.lower():
cacheusage = psutil.cached_phymem()
memusage = `psutil.phymem_usage()`.split(",")
freemem = long(memusage[2].split("free=")[-1])+long(cacheusage)
percentfree = float(memusage[3].split("percent=")[-1].split(")")[0])
avram = (freemem/1000000000)
print "[Available RAM: %d GB]"%(avram)
import os, sys, string, time, BaseHTTPServer, getopt, time, datetime, tempfile
#from datetime import date
#from ruffus import *
INITIAL_SRC = "%s%ssrc" % (sys.path[0], os.sep)
HOME_DIR = "%s" % (sys.path[0])
UTILS_DIR = "%s%sUtilities" % (sys.path[0], os.sep)
sys.path.insert(1, INITIAL_SRC)
import utils
import workflow
utils.configureEnvironment(utils.INITIAL_UTILS)
settings = utils.Settings(1, 1, "", "")
utils.getMachineType()
settings = utils.initConfig(1, 1, "", "", False, False, False, False, False)
#code to discover frozen binary location
application_path = ""
if getattr(sys, 'frozen', False):
application_path = os.path.dirname(sys.executable)
elif __file__:
application_path = os.path.dirname(__file__)
#code to update frozen binary runPipeline if newer one exists
try:
sys._MEIPASS
#print "Download/install latest version of MetAMOS frozen binary, if available? (note, this might require root/sudo access!)"
dl = 'y'
#dl = raw_input("Enter Y/N: ")
utils.run_process(settings, \
"rm %s/Assemble/out/*.asm.contig"%(settings.rundir),\
"RunPipeline")
if "Bin" not in skipsteps and "Bin" in forcesteps:
utils.run_process(settings, \
"rm %s/Logs/bin.ok"%(settings.rundir), \
"RunPipeline")
if __name__ == "__main__":
print "Starting metAMOS pipeline"
if settings.threads < 1:
settings.threads = 1
settings = utils.initConfig(settings.kmer, settings.threads,
settings.rundir, settings.taxa_level,
settings.local_krona,
settings.classify_unmapped,
settings.doscaffolding, settings.VERBOSE,
settings.OUTPUT_ONLY)
# add krona to system path
currPath = os.environ["PATH"]
if utils.Settings.KRONA not in currPath:
os.environ["PATH"] = "%s:%s" % (utils.Settings.KRONA, currPath)
# check for memory/cpu
if not settings.nopsutil and lowmem == False:
import psutil
avram = utils.getAvailableMemory(settings)
print "[Available RAM: %d GB]" % (avram)
lowmem = False
if avram <= 32:
aboutInfo = wx.adv.AboutDialogInfo()
aboutInfo.SetName("Pobkup")
aboutInfo.SetVersion(VERSION)
aboutInfo.SetIcon(wx.Icon('icons/icon.png', wx.BITMAP_TYPE_PNG))
aboutInfo.SetDescription(_("A simple gui for Rsync"))
aboutInfo.SetCopyright(
"Released under GNU/GPL v3 License \n\n Author: Fabio Di Matteo - [email protected]"
)
aboutInfo.SetWebSite("https://github.com/pobfdm/pobkup")
aboutInfo.AddDeveloper("Fabio Di Matteo - [email protected]")
aboutInfo.AddArtist(
"Arthur Zaynullin https://www.iconfinder.com/Ampeross")
wx.adv.AboutBox(aboutInfo)
if __name__ == '__main__':
#Gettext
try:
current_locale, encoding = locale.getdefaultlocale()
locale_path = 'locale'
language = gettext.translation('pobkup', locale_path, [current_locale])
language.install()
except:
print("Locale not found")
_ = gettext.gettext
utils.initConfig()
app = MainApp(False)
app.MainLoop()