# HG changeset patch
# User fubar
# Date 1412038065 14400
# Node ID ebadd2c92958f0b7ef072d263765a20d0e52c2fa
# Parent  84f6e67cbae57fb896b8b26256f9719cd817070c
Uploaded

diff -r 84f6e67cbae5 -r ebadd2c92958 data_manager/rnastar_index_builder.py
--- a/data_manager/rnastar_index_builder.py	Mon Sep 29 20:25:10 2014 -0400
+++ b/data_manager/rnastar_index_builder.py	Mon Sep 29 20:47:45 2014 -0400
@@ -43,7 +43,7 @@
          cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s
    --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' %  pdict
     elif sjdbFileChrStartEnd:
-        cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s'
+        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() )
@@ -104,6 +104,7 @@
       sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
       sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix,
       n_threads=options.runThreadN )
+
     
     #save info to json file
     open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
diff -r 84f6e67cbae5 -r ebadd2c92958 data_manager/rnastar_index_builder.xml
--- a/data_manager/rnastar_index_builder.xml	Mon Sep 29 20:25:10 2014 -0400
+++ b/data_manager/rnastar_index_builder.xml	Mon Sep 29 20:47:45 2014 -0400
@@ -6,7 +6,7 @@
     <command interpreter="python">
 rnastar_index_builder.py --out_file "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" 
 --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" 
---data_table_name "rnastar_indexes" --out_index_path "$out_file.extra_files_path" --runThreadN 1
+--data_table_name "rnastar_indexes" --out_index_path "${out_file.extra_files_path}" --runThreadN 1
 #if $genemodel.modelformat=="gff3":
  --sjdbOverhang "${genemodel.sjdbOverhang}"
  --sjdbGTFfile "${genemodel.sjdbGTFfile}"
diff -r 84f6e67cbae5 -r ebadd2c92958 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Sep 29 20:25:10 2014 -0400
+++ b/tool_data_table_conf.xml.sample	Mon Sep 29 20:47:45 2014 -0400
@@ -7,6 +7,6 @@
     <!-- Locations of indexes in the BWA mapper format -->
     <table name="rnastar_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/rnastar_index.loc" />
+        <file path="tool-data/rnastar_indexes.loc" />
     </table>
 </tables>