Mercurial > repos > iuc > data_manager_bwameth_index_builder
annotate data_manager/bwameth_index_builder.py @ 6:fca923910aaa draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author | iuc |
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date | Sun, 22 Nov 2020 12:46:50 +0000 |
parents | 5ab25caa7b7d |
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rev | line source |
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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1 #!/usr/bin/env python |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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2 # Based heavily on the HISAT2 data manager wrapper |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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3 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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4 import argparse |
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fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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5 import json |
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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6 import os |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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7 import subprocess |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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8 import sys |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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9 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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10 DEFAULT_DATA_TABLE_NAME = "bwameth_indexes" |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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11 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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12 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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13 def build_bwameth_index(data_manager_dict, params, args): |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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14 data_table_name = args.data_table_name |
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fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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15 target_directory = params['output_data'][0]['extra_files_path'] |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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16 if not os.path.exists(target_directory): |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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17 os.mkdir(target_directory) |
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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18 fasta_base_name = os.path.basename(args.fasta_filename) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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19 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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20 os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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21 cmd = ['bwameth.py', 'index', sym_linked_fasta_filename] |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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22 proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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23 return_code = proc.wait() |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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24 if return_code: |
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5ab25caa7b7d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
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25 print("Error building index.", file=sys.stderr) |
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fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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26 sys.exit(return_code) |
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e7ca32457e36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 471c497769f0dbfa92ec1a91f4044062cb5f7a83
iuc
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27 data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename) |
0
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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28 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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29 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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30 |
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fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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31 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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32 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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33 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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34 data_manager_dict['data_tables'][data_table_name].append(data_table_entry) |
0
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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35 return data_manager_dict |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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36 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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37 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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38 def main(): |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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39 # Parse Command Line |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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40 parser = argparse.ArgumentParser() |
6
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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41 parser.add_argument('--output', default=None) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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42 parser.add_argument('--fasta_filename', default=None) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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43 parser.add_argument('--dbkey', default=None) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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44 parser.add_argument('--name', default=None) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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45 parser.add_argument('--description', default=None) |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents:
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46 parser.add_argument('--data_table_name', default=DEFAULT_DATA_TABLE_NAME) |
0
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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47 args = parser.parse_args() |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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48 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
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49 filename = args.output |
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fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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50 with open(filename) as fh: |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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51 params = json.load(fh) |
0
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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52 data_manager_dict = {} |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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53 |
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fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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54 if args.dbkey in [None, '', '?']: |
0
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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55 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey)) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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56 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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57 # build the index |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
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58 build_bwameth_index(data_manager_dict, params, args) |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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59 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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60 # save info to json file |
6
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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61 with open(filename, 'w') as fh: |
fca923910aaa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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62 json.dump(data_manager_dict, fh, sort_keys=True) |
0
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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63 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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64 |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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65 if __name__ == "__main__": |
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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66 main() |