# HG changeset patch
# User dfornika
# Date 1551916363 18000
# Node ID 9d53c3f65ee60f5d4418a77e1f1ad6fa88e16c2a
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mash_sketch_refseq/ commit b12e918e7ed6127297b258843f9c107c40878881-dirty
diff -r 000000000000 -r 9d53c3f65ee6 data_manager/mash_build_sketch_refseq.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/mash_build_sketch_refseq.py Wed Mar 06 18:52:43 2019 -0500
@@ -0,0 +1,99 @@
+#!/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 = "mash_sketches"
+
+def run(args, cwd):
+ proc = subprocess.Popen(args=args, shell=False, cwd=cwd)
+ return_code = proc.wait()
+ if return_code:
+ print("Error building sketch.", file=sys.stderr)
+ sys.exit( return_code )
+
+def mash_build_sketch_refseq(data_manager_dict, sketch_type, target_directory, data_table_name=DATA_TABLE_NAME):
+
+ now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+ database_value = "_".join([
+ now,
+ "refseq" + "." +
+ sketch_type + "." +
+ "k21.s1000.msh",
+ ])
+
+ database_name = " ".join([
+ "refseq" + "." +
+ sketch_type + "." +
+ "k21.s1000.msh"
+ "(Created:",
+ now + ")"
+ ])
+
+ database_path = database_value
+
+ args = [
+ 'https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh'
+ ]
+
+ run(['wget'] + 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('--sketch-type', dest='sketch_type', help='Sketch Type (genome or plasmid or genome+plasmid)' )
+ parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
+
+ args = parser.parse_args()
+
+ 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 = {}
+
+ mash_build_sketch_refseq(
+ data_manager_output,
+ args.sketch_type,
+ target_directory,
+ )
+
+ open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 9d53c3f65ee6 data_manager/mash_build_sketch_refseq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/mash_build_sketch_refseq.xml Wed Mar 06 18:52:43 2019 -0500
@@ -0,0 +1,31 @@
+
+
+ database builder
+
+ mash
+
+ mash --version
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1186/gb-2014-15-3-r46
+
+
diff -r 000000000000 -r 9d53c3f65ee6 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Mar 06 18:52:43 2019 -0500
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+
diff -r 000000000000 -r 9d53c3f65ee6 tool-data/mash_sketches.loc.sample