## making ft_string to communicate it to dare
ft_step_string = ""
for i in range(0, len(num_step_wus)):
if (step_type[i] == "data"):
ft_step_string = ft_step_string + "step_" + str(i)
if (x != (num_step_wus[i] - 1)):
ft_step_string = ft_step_string + ", "
dare_config.set(section_name, "ft_steps", ft_step_string)
############### write the config file for dare.py #########################################
try:
dare_conffile = os.path.join(working_directory,
str(jobid) + "-darejob.cfg")
dare_cfgfile = open(dare_conffile, 'w')
dare_config.write(dare_cfgfile)
dare_cfgfile.close()
except:
print("Could not write DARE config file")
sys.exit(0)
#start dare
#print dare_conffile
#try:
dare_instance = dare(dare_conffile)
dare_instance.run()
#except :
# print "could not a start dare instance"
config.set(section_name, "environment","")
config.set(section_name, "working_directory", working_directory)
config.set(section_name, "output", os.path.join(working_directory, "stdout-"+ str(dare_uuid) +"-"+str(wus_count)+".txt"))
config.set(section_name, "error", os.path.join(working_directory, "stderr-"+ str(dare_uuid) +"-"+str(wus_count)+".txt" ))
config.set(section_name, "appname", "simple")
config.set(section_name, "resource" , 0)
wus_count = wus_count + 1
"""
step = step + 1
# ft after result. html
section_name = "wu_"+ str(wus_count)
config.add_section(section_name)
config.set(section_name, "appname", "file_transfer")
config.set(section_name, "fs_type", "scp")
config.set(section_name, "source_url", working_directory + "/tophatfusion_out/result.html")
config.set(section_name, "dest_url", "[email protected]:" +"/home/cctsg/install/DARE-NGS/darengs/templates/tophat_results/result_"+ jobid+ ".mako" )
wus_count = wus_count + 1
#write the config file
config.write(cfgfile)
cfgfile.close()
#start dare with above written config file
dare_instance = dare.dare()
dare_instance.run(dare_conffile)
ft_step_string = ""
for i in range (0, len(num_step_wus)):
if (step_type[i] == "data"):
ft_step_string = ft_step_string + "step_" + str(i)
if (x != (num_step_wus[i] -1)):
ft_step_string = ft_step_string + ", "
dare_config.set(section_name , "ft_steps", ft_step_string)
############### write the config file for dare.py #########################################
try:
dare_conffile = os.path.join(working_directory, str(jobid) +"-darejob.cfg")
dare_cfgfile = open(dare_conffile,'w')
dare_config.write(dare_cfgfile)
dare_cfgfile.close()
except:
print "Could not write DARE config file"
sys.exit(0);
#start dare
#print dare_conffile
#try:
dare_instance = dare(dare_conffile)
dare_instance.run()
#except :
# print "could not a start dare instance"
config.set(section_name, "environment","")
config.set(section_name, "working_directory", working_directory)
config.set(section_name, "output", os.path.join(working_directory, "stdout-"+ str(dare_uuid) +"-"+str(wus_count)+".txt"))
config.set(section_name, "error", os.path.join(working_directory, "stderr-"+ str(dare_uuid) +"-"+str(wus_count)+".txt" ))
config.set(section_name, "appname", "simple")
config.set(section_name, "resource" , 0)
wus_count = wus_count + 1
"""
step = step + 1
# ft after result. html
section_name = "wu_"+ str(wus_count)
config.add_section(section_name)
config.set(section_name, "appname", "file_transfer")
config.set(section_name, "fs_type", "scp")
config.set(section_name, "source_url", working_directory + "/tophatfusion_out/result.html")
config.set(section_name, "dest_url", "[email protected]:" +"/home/cctsg/install/DARE-NGS/darengs/templates/tophat_results/result_"+ jobid+ ".mako" )
wus_count = wus_count + 1
#write the config file
config.write(cfgfile)
cfgfile.close()
#start dare with above written config file
dare_instance = dare.dare()
dare_instance.run(dare_conffile)
