Mercurial > repos > iuc > data_manager_humann2_database_downloader

comparison data_manager/data_manager_humann2_download.py @ 2:6112a571f012 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit f474a24a52dcda7fb6681869e24f566d28f1e457
author iuc
date Fri, 23 Jun 2017 06:00:47 -0400
parents 048593e41359
children 9244804f69a7
comparison
equal deleted inserted replaced
1:1316375a8cbb 2:6112a571f012
3 # Data manager for reference data for the 'humann2' Galaxy tools 3 # Data manager for reference data for the 'humann2' Galaxy tools
4 import datetime 4 import datetime
5 import json 5 import json
6 import optparse 6 import optparse
7 import os 7 import os
8 import shutil
8 import subprocess 9 import subprocess
9 import sys 10 import sys
10 11
11 12
12 HUMANN2_REFERENCE_DATA = { 13 HUMANN2_REFERENCE_DATA = {
13 "full": "Full", 14 "full": "Full",
14 "DEMO": "Demo", 15 "DEMO": "Demo",
15 "uniref50_diamond": "Full UniRef50", 16 "uniref50_diamond": "Full UniRef50",
16 "uniref50_ec_filtered_diamond": "EC-filtered UniRef50", 17 "uniref50_ec_filtered_diamond": "EC-filtered UniRef50",
17 "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2", 18 "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2",
18 "uniref90_diamond": "Full UniRef50", 19 "uniref90_diamond": "Full UniRef90",
19 "uniref90_ec_filtered_diamond": "EC-filtered UniRef90", 20 "uniref90_ec_filtered_diamond": "EC-filtered UniRef90",
20 "DEMO_diamond": "Demo" 21 "DEMO_diamond": "Demo"
21 } 22 }
22 23
23 24
110 """ 111 """
111 value = "%s-%s-%s" % (database, build, datetime.date.today().isoformat()) 112 value = "%s-%s-%s" % (database, build, datetime.date.today().isoformat())
112 db_target_dir = os.path.join(target_dir, database) 113 db_target_dir = os.path.join(target_dir, database)
113 build_target_dir = os.path.join(db_target_dir, build) 114 build_target_dir = os.path.join(db_target_dir, build)
114 os.makedirs(build_target_dir) 115 os.makedirs(build_target_dir)
115 cmd = "humann2_databases --download %s %s %s" % (database, 116 cmd = "humann2_databases --download %s %s %s --update-config no" % (
116 build, 117 database,
117 db_target_dir) 118 build,
119 db_target_dir)
118 subprocess.check_call(cmd, shell=True) 120 subprocess.check_call(cmd, shell=True)
119 print(os.listdir(db_target_dir)) 121 shutil.move(os.path.join(db_target_dir, database), build_target_dir)
120 os.rename(os.path.join(db_target_dir, database), build_target_dir)
121 print(os.listdir(db_target_dir))
122 add_data_table_entry( 122 add_data_table_entry(
123 data_tables, 123 data_tables,
124 table_name, 124 table_name,
125 dict( 125 dict(
126 dbkey=build, 126 dbkey=build,