Use localhost by default for MongoDB address.

chipathlon/db.py

@@ -28,7 +28,7 @@ class MongoDB(object):
     operations much easier.
     """
 
-    def __init__(self, host, username, password, debug=False):
+    def __init__(self, host="localhost", username, password, debug=False):
         self.debug = debug
         self.host = host
         self.username = username

chipathlon/jobs/scripts/db_save_result.py

@@ -7,7 +7,7 @@ import os
 parser = argparse.ArgumentParser(description="Insert a bed file into the database.")
 parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
 parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
-parser.add_argument("-d", "--host", dest="host", required=True, help="Database host.")
+parser.add_argument("-d", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
 parser.add_argument("-f", "--file", dest="file", required=True, help="Path to result file.")
 parser.add_argument("-m", "--meta", dest="meta", required=True, help="Path to meta yaml file.")
 args = parser.parse_args()

chipathlon/jobs/scripts/download_from_gridfs.py

@@ -5,7 +5,7 @@ import argparse
 parser = argparse.ArgumentParser(description="Download target file from GridFS.")
 parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
 parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
-parser.add_argument("-H", "--host", dest="host", required=True, help="Database host.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
 parser.add_argument("-i", "--id", dest="gridfs_id", required=True, help="GridFS ID.")
 parser.add_argument("-d", "--destination", dest="destination", required=True, help="Local path to file destination.")
 parser.add_argument("-r", "--retries", dest="retries", default=3, type=int, help="Number of retries.")

scripts/chip-create-run

@@ -6,9 +6,9 @@ import yaml
 import pprint
 
 parser = argparse.ArgumentParser(description="Create a run file from a list of experiment accessions.")
-parser.add_argument("-H", "--host", dest="host", required=True, help="Database host.")
 parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
 parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
 parser.add_argument("-n", "--name", dest="name", required=True, help="Name of the run file to create.")
 parser.add_argument("-f", "--file_type", dest="file_type", default="fastq", help="Type of files to extract (fastq or bam).")
 

scripts/chip-gen

@@ -5,9 +5,9 @@ import yaml
 import pprint
 
 parser = argparse.ArgumentParser(description="Generates a workflow from a run, param & config file.")
-parser.add_argument("-H", "--host", dest="host", required=True, help="Database host.")
 parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
 parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
 parser.add_argument("-d", "--dir", dest="dir", required=True, help="Directory name to generate files in.")
 parser.add_argument("--param", dest="param", required=True, help="Path to param file to load.")
 parser.add_argument("--conf", dest="config", required=True, help="Path to config file to load.")

scripts/chip-meta-import

@@ -9,9 +9,9 @@ import os
 import os.path
 
 parser = argparse.ArgumentParser(description="Read per-experiment JSON files and create experiment and samples collections.")
-parser.add_argument("-H", "--host", dest="host", default="hcc-anvil-175-9.unl.edu", help="Database host. (default: %(default)s)")
 parser.add_argument("-u", "--username", dest="username", default="aknecht", required=True, help="Database user. (default: %(default)s)")
 parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
 parser.add_argument("-i", "--input-dir", dest="inputdir", default=os.getcwd(), help="Directory containing per-experiment JSON files.  (default: %(default)s)")
 parser.add_argument("-d", "--drop", dest="drop", default=False, action="store_true", help="Drop data if it exists. (default: %(default)s)")
 parser.add_argument("-s", "--samples", dest="samples", default=False, action="store_true", help="Only recreate the samples collection.")