Get SV_DIR from PATH

snakecnv/referencebundle.snk

@@ -17,6 +17,7 @@ configfile: "referencebundle.yaml"
 if not "SV_DIR" in os.environ:
     raise Exception("SV_DIR environment variable must be filled!")
 
+SV_DIR = os.environ['SV_DIR']
 CLASSPATH = SV_DIR + "/lib/SVToolkit.jar" + ":" + SV_DIR +"/lib/gatk/GenomeAnalysisTK.jar"
 ROOT_DIR = config['rootdir']
 WDIR = config['workdir']