Mercurial > repos > iuc > data_manager_dram_database_downloader
annotate data_manager/data_manager_dram_download.py @ 0:bd342a6a5b0f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
author | iuc |
---|---|
date | Thu, 01 Sep 2022 17:16:07 +0000 |
parents | |
children |
rev | line source |
---|---|
0
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
1 #!/usr/bin/env python |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
2 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
3 import argparse |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
4 import json |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
5 import os |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
6 import subprocess |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
7 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
8 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
9 parser = argparse.ArgumentParser() |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
10 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
11 parser.add_argument('--kofam_hmm_loc', action='store', dest='kofam_hmm_loc', default=None, help='hmm file for KOfam') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
12 parser.add_argument('--kofam_ko_list_loc', action='store', dest='kofam_ko_list_loc', default=None, help='KOfam ko list file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
13 parser.add_argument('--skip_uniref', action='store', dest='skip_uniref', default='no', help='Flag to Download and process uniref') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
14 parser.add_argument('--uniref_loc', action='store', dest='uniref_loc', default=None, help='uniref file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
15 parser.add_argument('--uniref_version', action='store', dest='uniref_version', type=int, default=90, help='uniref version to download') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
16 parser.add_argument('--pfam_loc', action='store', dest='pfam_loc', default=None, help='pfam-A full file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
17 parser.add_argument('--pfam_hmm_dat', action='store', dest='pfam_hmm_dat', help='pfam hmm .dat file to get PF descriptions') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
18 parser.add_argument('--dbcan_loc', action='store', dest='dbcan_loc', default=None, help='dbCAN file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
19 parser.add_argument('--dbcan_fam_activities', action='store', dest='dbcan_fam_activities', default=None, help='CAZY family activities file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
20 parser.add_argument('--dbcan_version', action='store', dest='dbcan_version', type=int, default=10, help='Version of dbCAN to use') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
21 parser.add_argument('--vogdb_loc', action='store', dest='vogdb_loc', default=None, help='hmm file for vogdb') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
22 parser.add_argument('--vog_annotations', action='store', dest='vog_annotations', default=None, help='vogdb annotations file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
23 parser.add_argument('--viral_loc', action='store', dest='viral_loc', default=None, help='merged viral protein faa file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
24 parser.add_argument('--peptidase_loc', action='store', dest='peptidase_loc', default=None, help='MEROPS peptidase fasta file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
25 parser.add_argument('--genome_summary_form_loc', action='store', dest='genome_summary_form_loc', default=None, help='genome summary form file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
26 parser.add_argument('--module_step_form_loc', action='store', dest='module_step_form_loc', default=None, help='module step form file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
27 parser.add_argument('--etc_module_database_loc', action='store', dest='etc_module_database_loc', default=None, help='etc module database file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
28 parser.add_argument('--function_heatmap_form_loc', action='store', dest='function_heatmap_form_loc', default=None, help='function heatmap form file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
29 parser.add_argument('--amg_database_loc', action='store', dest='amg_database_loc', default=None, help='amg database file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
30 parser.add_argument('--db_version', action='store', dest='db_version', help='Version of DRAM databases') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
31 parser.add_argument('--threads', action='store', dest='threads', type=int, help='Number of processes') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
32 parser.add_argument('--out_file', action='store', dest='out_file', help='JSON output file') |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
33 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
34 args = parser.parse_args() |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
35 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
36 with open(args.out_file) as fh: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
37 params = json.load(fh) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
38 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
39 target_directory = params['output_data'][0]['extra_files_path'] |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
40 os.makedirs(target_directory) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
41 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
42 # Download the data. |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
43 cmd = 'DRAM-setup.py prepare_databases --output_dir %s' % target_directory |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
44 if args.kofam_hmm_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
45 cmd = '%s --kofam_hmm_loc %s' % (cmd, args.kofam_hmm_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
46 if args.kofam_ko_list_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
47 cmd = '%s --kofam_ko_list_loc %s' % (cmd, args.kofam_ko_list_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
48 if args.skip_uniref == 'yes': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
49 cmd = '%s --skip_uniref' % cmd |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
50 else: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
51 if args.uniref_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
52 cmd = '%s --uniref_loc %s' % (cmd, args.uniref_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
53 cmd = '%s --uniref_version %d' % (cmd, args.uniref_version) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
54 if args.pfam_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
55 cmd = '%s --pfam_loc %s' % (cmd, args.pfam_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
56 if args.pfam_hmm_dat is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
57 cmd = '%s --pfam_hmm_dat %s' % (cmd, args.pfam_hmm_dat) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
58 if args.dbcan_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
59 cmd = '%s --dbcan_loc %s' % (cmd, args.dbcan_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
60 if args.dbcan_fam_activities is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
61 cmd = '%s --dbcan_fam_activities %s' % (cmd, args.dbcan_fam_activities) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
62 cmd = '%s --dbcan_version %d' % (cmd, args.dbcan_version) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
63 if args.vogdb_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
64 cmd = '%s --vogdb_loc %s' % (cmd, args.vogdb_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
65 if args.vog_annotations is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
66 cmd = '%s --vog_annotations %s' % (cmd, args.vog_annotations) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
67 if args.viral_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
68 cmd = '%s --viral_loc %s' % (cmd, args.viral_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
69 if args.peptidase_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
70 cmd = '%s --peptidase_loc %s' % (cmd, args.peptidase_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
71 if args.genome_summary_form_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
72 cmd = '%s --genome_summary_form_loc %s' % (cmd, args.genome_summary_form_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
73 if args.module_step_form_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
74 cmd = '%s --module_step_form_loc %s' % (cmd, args.module_step_form_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
75 if args.etc_module_database_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
76 cmd = '%s --etc_module_database_loc %s' % (cmd, args.etc_module_database_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
77 if args.function_heatmap_form_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
78 cmd = '%s --function_heatmap_form_loc %s' % (cmd, args.function_heatmap_form_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
79 if args.amg_database_loc is not None: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
80 cmd = '%s --amg_database_loc %s' % (cmd, args.amg_database_loc) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
81 cmd = '%s --threads %d' % (cmd, args.threads) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
82 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
83 subprocess.check_call(cmd, shell=True) |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
84 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
85 data_manager_json = {'data_tables': {}} |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
86 data_manager_entry = {} |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
87 data_manager_entry['value'] = args.db_version |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
88 data_manager_entry['name'] = 'DRAM %s databases' % args.db_version |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
89 data_manager_entry['path'] = target_directory |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
90 data_manager_json['data_tables']['dram_databases'] = data_manager_entry |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
91 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
92 with open(args.out_file, 'w') as fh: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
93 json.dump(data_manager_json, fh, sort_keys=True) |