Mercurial > repos > iuc > data_manager_kallisto_index_builder

annotate data_manager/kallisto_index_builder.py @ 0:6843a0db2da0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 04:02:01 -0400
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children 18e2dd472525
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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1 #!/usr/bin/env python
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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2 # Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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3 from __future__ import print_function
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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5 import argparse
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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6 import os
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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7 import subprocess
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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8 import sys
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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9 from json import dumps, loads
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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11 DEFAULT_DATA_TABLE_NAME = "kallisto_indexes"
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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14 def get_id_name( params, dbkey, fasta_description=None):
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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15 # TODO: ensure sequence_id is unique and does not already appear in location file
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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16 sequence_id = params['param_dict']['sequence_id']
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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17 if not sequence_id:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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18 sequence_id = dbkey
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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20 sequence_name = params['param_dict']['sequence_name']
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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21 if not sequence_name:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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22 sequence_name = fasta_description
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 if not sequence_name:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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24 sequence_name = dbkey
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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25 return sequence_id, sequence_name
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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28 def build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name ):
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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29 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 target_directory = params[ 'output_data' ][0]['extra_files_path']
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 if not os.path.exists( target_directory ):
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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32 os.mkdir( target_directory )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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33 fasta_base_name = os.path.split( options.fasta_filename )[-1]
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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34 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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35 os.symlink( options.fasta_filename, sym_linked_fasta_filename )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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36 args = [ 'kallisto', 'index' ]
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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37 args.extend( [ sym_linked_fasta_filename, '-i', sequence_id ] )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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38 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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39 return_code = proc.wait()
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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40 if return_code:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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41 print("Error building index.", file=sys.stderr)
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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42 sys.exit( return_code )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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43 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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44 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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47 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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48 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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49 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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50 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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51 return data_manager_dict
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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54 def main():
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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55 # Parse Command Line
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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56 parser = argparse.ArgumentParser()
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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57 parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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58 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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59 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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60 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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61 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='kallisto_indexes' )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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62 options = parser.parse_args()
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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64 filename = options.output
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66 params = loads( open( filename ).read() )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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67 data_manager_dict = {}
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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68
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69 if options.fasta_dbkey in [ None, '', '?' ]:
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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70 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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72 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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74 # build the index
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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75 build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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77 # save info to json file
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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78 open( filename, 'w' ).write( dumps( data_manager_dict ) )
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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79
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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80
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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81 if __name__ == "__main__":
6843a0db2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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82 main()