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Anonymous committed bb20a73

Fix genetree.commands.sh to call raxml with the correct flags

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Files changed (1)

agalma/genetree.py

 
 import glob
 import os
+import random
 
 from dendropy import Tree
 import numpy
 	with open('genetree.commands.sh', 'w') as f:
 		for phylip in glob.glob(os.path.join(phylip_dir, '*.phy')):
 			basename = os.path.splitext(os.path.basename(phylip))[0]
-			print >>f, '{0} {1} {2} {3} {4} {5} -T {6}'.format(
+			pars_rseed = random.randint(0,sys.maxint)
+			print >>f, '{0} -s {1} -n {2} -m {3} -w {4} {5} -T {6} -p {7}'.format(
 				config.get_command('raxml')[0], phylip, basename, model, 
-				all_trees_dir, raxml_flags, config.get_resource('threads'))
+				all_trees_dir, raxml_flags, config.get_resource('threads'),
+				pars_rseed)
 	# Run RAxML
 	wrappers.Parallel(
                 'genetree.commands.sh', '--joblog', 'genetree.commands.log', '--resume',