Mercurial > repos > dfornika > data_manager_build_kraken2_database
annotate data_manager/kraken2_build_standard.py @ 5:1f6fe9dc5490 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
author | dfornika |
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date | Mon, 04 Mar 2019 18:59:44 -0500 |
parents | 32d04371ed19 |
children | ae6180bdb1e9 |
rev | line source |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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1 #!/usr/bin/env python |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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2 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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3 from __future__ import print_function |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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4 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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5 import argparse |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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6 import datetime |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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7 import errno |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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8 import json |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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9 import os |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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10 import string |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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11 import subprocess |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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12 import sys |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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13 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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14 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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15 DATA_TABLE_NAME = "kraken2_databases" |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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16 |
5
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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17 def run(args, cwd): |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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18 proc = subprocess.Popen(args=args, shell=False, cwd=cwd) |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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19 return_code = proc.wait() |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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20 if return_code: |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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21 print("Error building database.", file=sys.stderr) |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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22 sys.exit( return_code ) |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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23 |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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24 def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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25 today = datetime.date.today().isoformat() |
5
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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26 database_name = "_".join([ |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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27 today, |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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28 "standard", |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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29 "kmer-len=" + str(kraken2_args["kmer_len"]), |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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30 "minimizer-len=" + str(kraken2_args["minimizer_len"]), |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
dfornika
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31 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]), |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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32 ]) |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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33 args = [ |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
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34 '--threads', str(kraken2_args["threads"]), |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
parents:
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35 '--standard', |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
parents:
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36 '--kmer-len', str(kraken2_args["kmer_len"]), |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
parents:
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37 '--minimizer-len', str(kraken2_args["minimizer_len"]), |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
parents:
diff
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38 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
dfornika
parents:
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39 '--db', database_name |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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40 ] |
5
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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41 |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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42 run(['kraken2-build'] + args, target_directory) |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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43 |
1
32d04371ed19
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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44 args = [ |
32d04371ed19
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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45 'kraken2-build', |
32d04371ed19
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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46 '--threads', str(kraken2_args["threads"]), |
32d04371ed19
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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47 '--clean', |
32d04371ed19
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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48 '--db', database_name |
32d04371ed19
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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49 ] |
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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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50 |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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51 run(['kraken2-build'] + args, target_directory) |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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52 |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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53 data_table_entry = { |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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54 "value": database_name, |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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55 "name": database_name, |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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56 "path": database_name |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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57 } |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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58 |
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1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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59 _add_data_table_entry(data_manager_dict, data_table_entry) |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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60 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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61 |
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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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62 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME): |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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63 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) |
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1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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64 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] ) |
1f6fe9dc5490
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
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65 data_manager_dict['data_tables'][data_table_name].append( data_table_entry ) |
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7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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66 return data_manager_dict |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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67 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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68 |
7e43f66abe9d
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
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69 def main(): |
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70 parser = argparse.ArgumentParser() |
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71 parser.add_argument('data_manager_json') |
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72 parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) |
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73 parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) |
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74 parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) |
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75 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) |
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76 args = parser.parse_args() |
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77 |
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78 kraken2_args = { |
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79 "kmer_len": args.kmer_len, |
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80 "minimizer_len": args.minimizer_len, |
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81 "minimizer_spaces": args.minimizer_spaces, |
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82 "threads": args.threads, |
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83 } |
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84 |
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85 data_manager_input = json.loads(open(args.data_manager_json).read()) |
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86 |
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87 target_directory = data_manager_input['output_data'][0]['extra_files_path'] |
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88 |
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89 try: |
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90 os.mkdir( target_directory ) |
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91 except OSError as exc: |
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92 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): |
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93 pass |
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94 else: |
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95 raise |
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96 |
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97 kraken2_build_standard( |
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98 data_manager_input, |
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99 kraken2_args, |
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100 target_directory, |
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101 ) |
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102 |
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103 open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input)) |
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104 |
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105 |
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106 if __name__ == "__main__": |
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107 main() |