Anonymous avatar Anonymous committed 78f14f5

RAxML now uses Parallel; failed runs will be skipped [issue#61]

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Files changed (3)

-INSTALL.md

agalma/genetree.py

 		# Configure raxml to run both bootstraps and ml
 		seed = 12345
 		raxml_flags = '-f a -N {0} -x {1} '.format(bootstrap, seed) + raxml_flags
-
-	for phylip in glob.glob(os.path.join(phylip_dir, '*.phy')):
-		basename = os.path.splitext(os.path.basename(phylip))[0]
-		wrappers.Raxml(phylip, basename, model, all_trees_dir, extra_flags=raxml_flags)
+	
+	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(
+				config.get_command('raxml')[0], phylip, basename, model, 
+				all_trees_dir, extra_flags=raxml_flags, config.get_resource('threads'))
+	# Run RAxML
+	wrappers.Parallel(
+                'genetree.commands.sh', '--joblog', 'genetree.commands.log', '--resume',
+                return_ok=None, threads=1)
 
 	diagnostics.log('raxml_dir', all_trees_dir)
 	ingest('all_trees_dir')

autom4te.cache/traces.1

-m4trace:aclocal.m4:944: -1- m4_include([m4/ac_define_dir.m4])
+m4trace:aclocal.m4:906: -1- m4_include([m4/ac_define_dir.m4])
 m4trace:configure.ac:5: -1- AC_INIT([agalma], [0.3.3], [mhowison@brown.edu])
 m4trace:configure.ac:5: -1- m4_pattern_forbid([^_?A[CHUM]_])
 m4trace:configure.ac:5: -1- m4_pattern_forbid([_AC_])
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