Mercurial > repos > devteam > data_manager_bwa_index_builder
changeset 1:cc5ae94acf01 draft default tip
planemo upload commit 2b9ef766ea9ee24964464363a9d41faeefa3d360-dirty
| author | devteam |
|---|---|
| date | Wed, 26 Aug 2015 11:50:48 -0400 |
| parents | 367878cb3698 |
| children | |
| files | data_manager/bwa_index_builder.py data_manager/bwa_index_builder.xml tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 15 deletions(-) [+] |
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--- a/data_manager/bwa_index_builder.py Fri Mar 28 14:18:43 2014 -0400 +++ b/data_manager/bwa_index_builder.py Wed Aug 26 11:50:48 2015 -0400 @@ -7,7 +7,7 @@ import optparse import subprocess -from galaxy.util.json import from_json_string, to_json_string +from json import loads, dumps CHUNK_SIZE = 2**20 @@ -46,20 +46,11 @@ if color_space: args.append( '-c' ) args.append( sym_linked_fasta_filename ) - tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-bwa-index-builder-stderr" ) - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait() if return_code: - tmp_stderr.flush() - tmp_stderr.seek(0) - print >> sys.stderr, "Error building index:" - while True: - chunk = tmp_stderr.read( CHUNK_SIZE ) - if not chunk: - break - sys.stderr.write( chunk ) + print >> sys.stderr, "Error building index." sys.exit( return_code ) - tmp_stderr.close() data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) @@ -81,7 +72,7 @@ filename = args[0] - params = from_json_string( open( filename ).read() ) + params = loads( open( filename ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) data_manager_dict = {} @@ -97,6 +88,6 @@ build_bwa_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space ) #save info to json file - open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) + open( filename, 'wb' ).write( dumps( data_manager_dict ) ) if __name__ == "__main__": main()
--- a/data_manager/bwa_index_builder.xml Fri Mar 28 14:18:43 2014 -0400 +++ b/data_manager/bwa_index_builder.xml Wed Aug 26 11:50:48 2015 -0400 @@ -4,6 +4,10 @@ <requirement type="package" version="0.5.9">bwa</requirement> </requirements> <command interpreter="python">bwa_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bwa_indexes"</command> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> <inputs> <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta"/>
--- a/tool_dependencies.xml Fri Mar 28 14:18:43 2014 -0400 +++ b/tool_dependencies.xml Wed Aug 26 11:50:48 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="bwa" version="0.5.9"> - <repository changeset_revision="ec2595e4d313" name="package_bwa_0_5_9" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ec2595e4d313" name="package_bwa_0_5_9" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>