def backend_assembly(new_filename, user_email, pipeline_num, tools,
file1_location, download_folder):
print("running assembly back_end.....")
print("tools are " + str(tools))
flag = 0
# MAKE OUTPUT PATH SPECIFIC FOR YOUR TOOL THIS IS JUST A TEST OUTPUT PATH
pool.apply_async(genomeassembly.f,
(file1_location, flag, download_folder, tools))
if flag == 0:
c1 = db_util.scolia_data(job_id=new_filename,
email=user_email,
job_submitted=0,
email_sent=0,
pipeline_number=pipeline_num)
db_util.insert(c1)
return (True)
def backend_function(new_filename, user_email, pipeline_num, tools,
file1_location, download_folder):
print(tools)
flag = 0
pool.apply_async(functional_annotation_pipeline.f, (
file1_location,
download_folder,
flag,
))
if flag == 0:
c1 = db_util.scolia_data(job_id=new_filename,
email=user_email,
job_submitted=0,
email_sent=0,
pipeline_number=pipeline_num)
db_util.insert(c1)
return (True)
def backend_comparative_no_reference(new_filename, user_email, pipeline_num,
tools, file1_location, download_folder):
flag = 0
#MAKE OUTPUT PATH SPECIFIC FOR YOUR TOOL THIS IS JUST A TEST OUTPUT PATH
subprocess.run("mkdir " + BASE_OUTPUT_PATH + "Comparitive_Genomics/" +
new_filename,
shell=True)
output_path = BASE_OUTPUT_PATH + "Comparative_Genomics/" + new_filename + ".tar.gz"
#THIS IS JUST AN EXAMPLE FUNCTION
pool.apply_async(models.f, (10, file1_location, flag, output_path))
if flag == 0:
c1 = db_util.scolia_data(job_id=new_filename,
email=user_email,
job_submitted=0,
email_sent=0,
pipeline_number=pipeline_num)
db_util.insert(c1)
return (True)
def backend_function(new_filename, user_email, pipeline_num, tools,
file1_location, download_folder):
print(tools)
flag = 0
#subprocess.run("mkdir "+BASE_OUTPUT_PATH+"Functional_Annotation/"+new_filename, shell = True)
#output_path=BASE_OUTPUT_PATH+"Functional_Annotation/"+new_filename+".tar.gz"
pool.apply_async(functional_annotation_pipeline.f, (
file1_location,
download_folder,
flag,
))
if flag == 0:
c1 = db_util.scolia_data(job_id=new_filename,
email=user_email,
job_submitted=0,
email_sent=0,
pipeline_number=pipeline_num)
db_util.insert(c1)
return (True)
def backend_assembly(new_filename, user_email, pipeline_num, tools,
file1_location, download_folder):
print("running assembly back_end.....")
print("tools are " + str(tools))
flag = 0
# MAKE OUTPUT PATH SPECIFIC FOR YOUR TOOL THIS IS JUST A TEST OUTPUT PATH
#subprocess.run("mkdir " + BASE_OUTPUT_PATH + "Genome_Assembly/" + new_filename, shell=True)
#output_path = BASE_OUTPUT_PATH + "Genome_Assembly/" + new_filename + ".tar.gz"
#print("this is the output_path"+output_path)
# THIS IS JUST AN EXAMPLE FUNCTION
pool.apply_async(genomeassembly.f,
(file1_location, flag, download_folder, tools))
if flag == 0:
c1 = db_util.scolia_data(job_id=new_filename,
email=user_email,
job_submitted=0,
email_sent=0,
pipeline_number=pipeline_num)
db_util.insert(c1)
return (True)
def backend_prediction(new_filename, user_email, pipeline_num, tools,
file1_location, file2_location, download_folder):
flag = 0
#MAKE OUTPUT PATH SPECIFIC FOR YOUR TOOL THIS IS JUST A TEST OUTPUT PATH
subprocess.run("mkdir " + BASE_OUTPUT_PATH + "Gene_Prediction/" +
new_filename,
shell=True)
output_path = BASE_OUTPUT_PATH + "Gene_Prediction/" + new_filename + ".tar.gz"
#THIS IS JUST AN EXAMPLE FUNCTION
pool.apply_async(gene_prediction.f, (
file1_location,
file2_location,
download_folder,
flag,
))
if flag == 0:
c1 = db_util.scolia_data(job_id=new_filename,
email=user_email,
job_submitted=0,
email_sent=0,
pipeline_number=pipeline_num)
db_util.insert(c1)
return (True)