|
2
|
1
|
|
|
2 diff -r ebadd2c92958 data_manager/rnastar_index_builder.py
|
|
|
3 --- a/data_manager/rnastar_index_builder.py Mon Sep 29 20:47:45 2014 -0400
|
|
|
4 +++ b/data_manager/rnastar_index_builder.py Fri Oct 03 13:35:35 2014 -0400
|
|
|
5 @@ -9,7 +9,7 @@
|
|
|
6 import optparse
|
|
|
7 import subprocess
|
|
|
8
|
|
|
9 -from galaxy.util.json import from_json_string, to_json_string
|
|
|
10 +from json import loads, dumps
|
|
|
11
|
|
|
12 DEFAULT_DATA_TABLE_NAME = "rnastar_indexes"
|
|
|
13
|
|
|
14 @@ -44,20 +44,11 @@
|
|
|
15 --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict
|
|
|
16 elif sjdbFileChrStartEnd:
|
|
|
17 cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
|
|
|
18 - tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
|
|
|
19 args = cl.split(' ')
|
|
|
20 - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
|
|
|
21 + proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
|
|
|
22 return_code = proc.wait()
|
|
|
23 if return_code:
|
|
|
24 - tmp_stderr.flush()
|
|
|
25 - tmp_stderr.seek(0)
|
|
|
26 - print >> sys.stderr, "Error building index: retcode=",retcode
|
|
|
27 - while True:
|
|
|
28 - chunk = tmp_stderr.read( CHUNK_SIZE )
|
|
|
29 - if not chunk:
|
|
|
30 - break
|
|
|
31 - sys.stderr.write( chunk )
|
|
|
32 - tmp_stderr.close()
|
|
|
33 + sys.exit( return_code )
|
|
|
34 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
|
|
|
35 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
|
|
|
36
|
|
|
37 @@ -86,7 +77,7 @@
|
|
|
38 (options, args) = parser.parse_args()
|
|
|
39
|
|
|
40 filename = options.out_file
|
|
|
41 - params = from_json_string( open( filename ).read() )
|
|
|
42 + params = loads( open( filename ).read() )
|
|
|
43 target_directory = options.out_index_path
|
|
|
44 os.mkdir( target_directory )
|
|
|
45 data_manager_dict = {}
|
|
|
46 @@ -107,6 +98,7 @@
|
|
|
47
|
|
|
48
|
|
|
49 #save info to json file
|
|
|
50 - open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
|
|
|
51 + open( filename, 'wb' ).write( dumps( data_manager_dict ) )
|
|
|
52
|
|
|
53 if __name__ == "__main__": main()
|
|
|
54 +
|
|
|
55 diff -r ebadd2c92958 data_manager/rnastar_index_builder.xml
|
|
|
56 --- a/data_manager/rnastar_index_builder.xml Mon Sep 29 20:47:45 2014 -0400
|
|
|
57 +++ b/data_manager/rnastar_index_builder.xml Fri Oct 03 13:35:35 2014 -0400
|
|
|
58 @@ -22,7 +22,8 @@
|
|
|
59 #end if
|
|
|
60 </command>
|
|
|
61 <stdio>
|
|
|
62 - <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/>
|
|
|
63 + <exit_code range=":-1" err_level="fatal" />
|
|
|
64 + <exit_code range="1:" err_level="fatal" />
|
|
|
65 </stdio>
|
|
|
66
|
|
|
67 <inputs>
|
|
|
68 @@ -124,3 +125,4 @@
|
|
|
69
|
|
|
70 </help>
|
|
|
71 </tool>
|
|
|
72
|
