--- a/cummeRbund_options.py	Fri Mar 13 15:30:17 2015 -0400
+++ b/cummeRbund_options.py	Mon Mar 16 15:43:02 2015 -0400
@@ -1,23 +1,11 @@
-from galaxy import eggs
-eggs.require( 'SQLAlchemy' )
-eggs.require( 'pysqlite>=2' )
-from sqlalchemy import *
-from sqlalchemy.sql import and_
-from sqlalchemy.orm import sessionmaker
-from sqlalchemy.orm import scoped_session
+import sqlite3
 
 def get_genes( database_path ):
-    dburi = 'sqlite:///%s' % database_path
-    engine = create_engine( dburi )
-    meta = MetaData( bind=engine )
-    db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
-    gene_ids = db_session.execute( 'select gene_short_name, gene_id from genes order by gene_short_name' )
+    conn = sqlite3.connect( database_path )
+    gene_ids = conn.execute( 'SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name' )
     return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ]
 
 def get_samples( database_path ):
-    dburi = 'sqlite:///%s' % database_path
-    engine = create_engine( dburi )
-    meta = MetaData( bind=engine )
-    db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
-    samples = db_session.execute( 'select sample_name from samples order by sample_name' )
+    conn = sqlite3.connect( database_path )
+    samples = conn.execute( 'SELECT sample_name FROM samples ORDER BY sample_name' )
     return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ]