Mercurial > repos > iuc > data_manager_bowtie_index_builder

comparison data_manager/bowtie_index_builder.py @ 2:086edfff112b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 356a04ca3fb988f20fb63ccf053ef9f62a3d002f
author iuc
date Sun, 18 Sep 2016 08:21:09 -0400
parents 35c1e3785c90
children ea5faedd0795
comparison
equal deleted inserted replaced
1:35c1e3785c90 2:086edfff112b
30 fasta_base_name = os.path.split( fasta_filename )[-1] 30 fasta_base_name = os.path.split( fasta_filename )[-1]
31 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) 31 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
32 os.symlink( fasta_filename, sym_linked_fasta_filename ) 32 os.symlink( fasta_filename, sym_linked_fasta_filename )
33 args = [ 'bowtie-build' ] 33 args = [ 'bowtie-build' ]
34 if color_space: 34 if color_space:
35 args.append( '-c' ) 35 args.append( '-C' )
36 args.append( sym_linked_fasta_filename) 36 args.append( sym_linked_fasta_filename)
37 args.append( fasta_base_name ) 37 args.append( fasta_base_name )
38 args.append( sym_linked_fasta_filename ) 38 args.append( sym_linked_fasta_filename )
39 tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-bowtie-index-builder-stderr" ) 39 tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-bowtie-index-builder-stderr" )
40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) 40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )