diff danfix.patch @ 2:8a2d16bfdae2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/danfix.patch	Fri Oct 03 21:59:39 2014 -0400
@@ -0,0 +1,72 @@
+
+diff -r ebadd2c92958 data_manager/rnastar_index_builder.py
+--- a/data_manager/rnastar_index_builder.py Mon Sep 29 20:47:45 2014 -0400
++++ b/data_manager/rnastar_index_builder.py Fri Oct 03 13:35:35 2014 -0400
+@@ -9,7 +9,7 @@
+ import optparse
+ import subprocess
+
+-from galaxy.util.json import from_json_string, to_json_string
++from json import loads, dumps
+
+ DEFAULT_DATA_TABLE_NAME = "rnastar_indexes"
+
+@@ -44,20 +44,11 @@
+    --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' %  pdict
+     elif sjdbFileChrStartEnd:
+         cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
+-    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
+     args = cl.split(' ')
+-    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: retcode=",retcode
+-        while True:
+-            chunk = tmp_stderr.read( CHUNK_SIZE )
+-            if not chunk:
+-                break
+-            sys.stderr.write( chunk )
+-    tmp_stderr.close()
++        sys.exit( return_code )
+     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 )
+
+@@ -86,7 +77,7 @@
+     (options, args) = parser.parse_args()
+
+     filename = options.out_file
+-    params = from_json_string( open( filename ).read() )
++    params = loads( open( filename ).read() )
+     target_directory = options.out_index_path
+     os.mkdir( target_directory )
+     data_manager_dict = {}
+@@ -107,6 +98,7 @@
+
+
+     #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 ebadd2c92958 data_manager/rnastar_index_builder.xml
+--- a/data_manager/rnastar_index_builder.xml    Mon Sep 29 20:47:45 2014 -0400
++++ b/data_manager/rnastar_index_builder.xml    Fri Oct 03 13:35:35 2014 -0400
+@@ -22,7 +22,8 @@
+ #end if
+ </command>
+     <stdio>
+-        <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/>
++        <exit_code range=":-1" err_level="fatal" />
++        <exit_code range="1:" err_level="fatal" />
+     </stdio>
+
+     <inputs>
+@@ -124,3 +125,4 @@
+
+     </help>
+ </tool>
+