diff data_manager/rnastar_index_builder.xml @ 1:ebadd2c92958 draft

Uploaded
author fubar
date Mon, 29 Sep 2014 20:47:45 -0400
parents 84f6e67cbae5
children 8a2d16bfdae2
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line diff
--- 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}"