--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_minikraken.py	Tue Mar 05 14:33:23 2019 -0500
@@ -0,0 +1,130 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import errno
+import json
+import os
+import string
+import subprocess
+import sys
+
+
+DATA_TABLE_NAME = "kraken2_databases"
+
+def run(args, cwd):
+    proc = subprocess.Popen(args=args, shell=False, cwd=cwd)
+    return_code = proc.wait()
+    if return_code:
+        print("Error building database.", file=sys.stderr)
+        sys.exit( return_code )
+
+def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+    
+    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+    special_database_names = {
+        "rdp": "RDP",
+        "greengenes": "Greengenes",
+        "silva": "Silva",
+    }
+    
+    database_value = "_".join([
+        now,
+        kraken2_args["special"],
+        "kmer-len", str(kraken2_args["kmer_len"]),
+        "minimizer-len", str(kraken2_args["minimizer_len"]),
+        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+    ])
+
+    database_name = " ".join([
+        special_database_names[kraken2_args["special"]],
+        "(Created:",
+        now + ","
+        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
+        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
+        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+    ])
+
+    database_path = database_value
+    
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--special', kraken2_args["special"],
+        '--kmer-len', str(kraken2_args["kmer_len"]),
+        '--minimizer-len', str(kraken2_args["minimizer_len"]),
+        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--db', database_path
+    ]
+
+    run(['kraken2-build'] + args, target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--clean',
+        '--db', database_path
+    ]
+
+    run(['kraken2-build'] + args, target_directory)
+
+    data_table_entry = {
+        "value": database_value,
+        "name": database_name,
+        "path": database_path,
+    }
+    
+    _add_data_table_entry(data_manager_dict, data_table_entry)
+
+
+def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+    return data_manager_dict
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('data_manager_json')
+    parser.add_argument( '-b', '--db-type', dest='db_type', help='database type (one of: silva, rdp, greengenes)' )
+    parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' )
+    parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' )
+    parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' )
+    parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
+    args = parser.parse_args()
+
+    kraken2_args = {
+        "special": args.db_type,
+        "kmer_len": args.kmer_len,
+        "minimizer_len": args.minimizer_len,
+        "minimizer_spaces": args.minimizer_spaces,
+        "threads": args.threads,
+    }
+    
+    data_manager_input = json.loads(open(args.data_manager_json).read())
+
+    target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+    try:
+        os.mkdir( target_directory )
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+            pass
+        else:
+            raise
+
+    data_manager_output = {}
+    
+    kraken2_build_standard(
+        data_manager_output,
+        kraken2_args,
+        target_directory,
+    )
+
+    open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
+
+
+if __name__ == "__main__":
+    main()