Mercurial > repos > fubar > data_manager_rnasta
comparison danfix.patch @ 2:8a2d16bfdae2 draft
Uploaded
author | fubar |
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date | Fri, 03 Oct 2014 21:59:39 -0400 |
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1:ebadd2c92958 | 2:8a2d16bfdae2 |
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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 |