Mercurial > repos > iuc > data_manager_dram_database_downloader

annotate data_manager/data_manager_dram_download.py @ 1:40c8fc0a2bb0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
author iuc
date Tue, 13 Sep 2022 09:08:55 +0000
parents bd342a6a5b0f
children
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bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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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
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2
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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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
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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
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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
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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
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7
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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8
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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33
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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
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35
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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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
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38
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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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
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41
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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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
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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
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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
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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
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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
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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
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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
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50 else:
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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82
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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84
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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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
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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
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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
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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
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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
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91
bd342a6a5b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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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
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93 json.dump(data_manager_json, fh, sort_keys=True)