#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def TCGA_download(sample, TCGA_download_flag):
'''Downloads and unzips TCGA data from Manifest.xml downloaded from CGHub.
input:
TGCA XML file
output:
downloaded files from TCGA
citation:
The Cancer Genome Atlas
link:
https://cghub.ucsc.edu/software/downloads.html
parameters from parameters file:
TCGA_XML_FILE:
TCGA_KEY:
TCGA_OUTPUT_PATH:
CGATOOLS_VERSION:
'''
spawn_job(jobname = 'TCGA_download', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 8, memory = "31gb", script = "/TCGA_download.sh", args_list = [str(sample),p.TCGA_KEY,p.TCGA_OUTPUT_PATH,p.CGATOOLS_VERSION])
job_status(jobname = 'TCGA_download', resultspath = p.TCGA_OUTPUT_PATH, SAMPLE = sample, outputfilename = sample + "_1.fastq", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
TCGA_download(sample, TCGA_download_flag)
sys.exit(0)