Mercurial > repos > fubar > data_manager_rnasta

comparison danfix.patch @ 2:8a2d16bfdae2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Fri, 03 Oct 2014 21:59:39 -0400
parents
children
comparison
equal deleted inserted replaced
1:ebadd2c92958 2:8a2d16bfdae2
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