Mercurial > repos > devteam > data_manager_picard_index_builder

comparison data_manager/picard_index_builder.py @ 2:b99040168706 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 59ee07d9786f1a090053b4a13192247872389d61
author iuc
date Mon, 10 Apr 2017 06:06:23 -0400
parents dc28cd6a1d44
children ae080ff506fd
comparison
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1:dc28cd6a1d44 2:b99040168706
29 # TODO: allow multiple FASTA input files 29 # TODO: allow multiple FASTA input files
30 fasta_base_name = os.path.split( fasta_filename )[-1] 30 fasta_base_name = os.path.split( fasta_filename )[-1]
31 prefix = os.path.splitext( fasta_base_name )[0] 31 prefix = os.path.splitext( fasta_base_name )[0]
32 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) 32 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
33 os.symlink( fasta_filename, sym_linked_fasta_filename ) 33 os.symlink( fasta_filename, sym_linked_fasta_filename )
34 args = [ 'java', '-Xmx4G', '-jar', os.path.join( os.environ[ 'JAVA_JAR_PATH' ], 'CreateSequenceDictionary.jar' ), 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ] 34 args = [ 'picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ]
35 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) 35 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
36 return_code = proc.wait() 36 return_code = proc.wait()
37 if return_code: 37 if return_code:
38 print("Error building index.", file=sys.stderr) 38 print("Error building index.", file=sys.stderr)
39 sys.exit( return_code ) 39 sys.exit( return_code )