# HG changeset patch
# User devteam
# Date 1440604248 14400
# Node ID cc5ae94acf01d628ad11495d31139ecbfe614d34
# Parent 367878cb3698177bfbd8c132637f9e8172bd0dbd
planemo upload commit 2b9ef766ea9ee24964464363a9d41faeefa3d360-dirty
diff -r 367878cb3698 -r cc5ae94acf01 data_manager/bwa_index_builder.py
--- 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()
diff -r 367878cb3698 -r cc5ae94acf01 data_manager/bwa_index_builder.xml
--- 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 @@
bwa
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"
+
+
+
+
diff -r 367878cb3698 -r cc5ae94acf01 tool_dependencies.xml
--- 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 @@
-
+