Changed overwrite default to True. Adjusted download to the correct md5 value.

chipathlon/jobs/scripts/download_fastq.py

@@ -7,7 +7,7 @@ parser.add_argument("-u", "--url", dest="url", required=True, help="Target url."
 parser.add_argument("-p", "--path", dest="path", required=True, help="Local path to file.")
 parser.add_argument("-t", "--url_type", dest="url_type", default="ftp://", help="Type of url to access.")
 parser.add_argument("-r", "--retries", dest="retries", default=3, type=int, help="Number of retries.")
-parser.add_argument("-o", "--overwrite", dest="overwrite", default=False, action="store_true", help="Overwrite local file if exists.")
+parser.add_argument("-n", "--overwrite", dest="overwrite", default=True, action="store_false", help="Dont' overwrite local file if exists.")
 parser.add_argument("-m", "--md5", dest="md5", help="Check md5 value against passed value.")
 args = parser.parse_args()
 

chipathlon/utils.py

@@ -13,7 +13,7 @@ def progress(current, end, length=20):
     sys.stdout.flush()
 
 
-def downloadFile(url, localpath, urltype="ftp://", retries=3, overwrite=False, checkmd5=False, md5=None):
+def downloadFile(url, localpath, urltype="ftp://", retries=3, overwrite=True, checkmd5=False, md5=None):
     success = False
     if url[:7] == "http://":
         urltype = ""

chipathlon/workflow.py

@@ -253,7 +253,7 @@ class Workflow(object):
                         self.files[output_name] = output_file
                         job = Job(self.executables["download_fastq.py"])
                         job.uses(output_file, link=Link.OUTPUT, transfer=True)
-                        job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["content_md5sum"])
+                        job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["md5sum"])
                         self.jobs[output_name] = job
                         self.dax.addJob(job)
         return