Fixed number of threads

SConstruct

@@ -29,7 +29,7 @@ if env.GetOption('num_jobs') <= 1:
 	env.SetOption('num_jobs', num_cpu)
 	num_threads = num_cpu/4
 else:
-	num_threads = env.GetOption('num_jobs')
+	num_threads = num_cpu/env.GetOption('num_jobs')
 print "running with -j", GetOption('num_jobs')
 # Set number of simultaneous threads to something less than the number of CPUs
 # /CPUs
@@ -50,11 +50,11 @@ print "running with -j", GetOption('num_jobs')
 #ASSEMBLY = "/home/assembly/dev_150/assemblies/clc-default/clc_contigs.fa"
 #PREFIX   = "clc"
 
-ASSEMBLY = "/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw_with454/sl/data/run/ASSEMBLIES/test/final.assembly.fasta"
-PREFIX   = "allpaths_lg_454"
+#ASSEMBLY = "/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw_with454/sl/data/run/ASSEMBLIES/test/final.assembly.fasta"
+#PREFIX   = "allpaths_lg_454"
 
-#ASSEMBLY = "/home/assembly/dev_150/assemblies/S_lycopersicum_scaffolds.2.40.fa"
-#PREFIX   = "heinz"
+ASSEMBLY = "/home/assembly/dev_150/assemblies/S_lycopersicum_scaffolds.2.40.fa"
+PREFIX   = "heinz"
 
 #ASSEMBLY = "/home/assembly/progs/fermi/heinz/fmdef.p4.fa"
 #PREFIX   = "fermi"
@@ -108,7 +108,7 @@ def addCommand(cmd, data):
 
 #DATABASE
 bwtFile = "%s.bwt" % PREFIX
-bwtRes  = addCommand("bwa index -a is -p %(TARGET)s %(SOURCE)s", {"TARGET": PREFIX, "SOURCE": ASSEMBLY})
+bwtRes  = addCommand("bwa index -a is -p %(BWT_PREFIX)s %(SOURCE)s", {"BWT_PREFIX": PREFIX, "TARGET": bwtFile, "SOURCE": ASSEMBLY})
 
 
 #SETUP