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MUSCLE is now the default merger tool, and default memory is 1024MB

This should make it easier to use on Windows (no default java, and 32-bit java
cannot be given more than 2G RAM).
Also back propagated Siavash's changes to settings.py into the source
(the sate_ui.xml file).
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1 parent 8a5b596 commit 34ebb916f380632a1e7098d7607c0bd6ec621da9 @mtholder mtholder committed May 20, 2012
Showing with 15 additions and 9 deletions.
  1. +1 −1 run_sate_gui.py
  2. +1 −1 sate/mainsate.py
  3. +2 −2 sate/settings.py
  4. +11 −5 sate_ui.xml
View
2 run_sate_gui.py
@@ -255,7 +255,7 @@ def _create_tools_sizer(self):
if GLOBAL_DEBUG:
defaults = {"Aligner":"PADALIGNER", "Merger":"PADALIGNER", "TreeEstimator":"RANDTREE"}
else:
- defaults = {"Aligner":"MAFFT", "Merger":"OPAL", "TreeEstimator":"FASTTREE"}
+ defaults = {"Aligner":"MAFFT", "Merger":"MUSCLE", "TreeEstimator":"FASTTREE"}
self.cb_tools = {}
for item_idx, item in enumerate(items):
text = wx.StaticText(self, -1, "Tree Estimator") if item == "TreeEstimator" else wx.StaticText(self, -1, item)
View
2 sate/mainsate.py
@@ -86,7 +86,7 @@ def get_auto_defaults_from_summary_stats(datatype, ntax_nchar_tuple_list, total_
new_sate_defaults = {
'tree_estimator' : 'fasttree',
'aligner' : 'mafft',
- 'merger' : 'opal',
+ 'merger' : 'muscle',
'break_strategy' : 'longest',
'move_to_blind_on_worse_score' : True,
'start_tree_search_from_current' : True,
View
4 sate/settings.py
@@ -70,9 +70,9 @@ def __init__(self):
self.commandline.add_option('missing', ChoiceUserSetting(name='missing', default=None, choices=['Ambiguous', 'Absent'], multiple_choices=False, short_name=None, help='How to deal with missing data symbols. Specify either "Ambiguous" or "Absent" if the input data contains ?-symbols', subcategory=None))
self.commandline.add_option('auto', BoolUserSetting(name='auto', default='False', short_name=None, help='If used, then default values for the max_subproblem_size and tools will be used based on the dataset size. WARNING: using this option can cause SATe to override some of the other options that you have supplied; we recommend that you run this option with --exportconfig to see the exact set of options that will be used in your analysis.', subcategory=None))
self.sate.add_option('num_cpus', IntUserSetting(name='num_cpus', default=1, min=1, max=None, short_name=None, help='The number of processing cores that you would like to assign to SATe. This number should not exceed the number of cores on your machine.', subcategory='platform'))
- self.sate.add_option('max_mem_mb', IntUserSetting(name='max_mem_mb', default=2048, min=1024, max=None, short_name=None, help='The maximum memory available (for the Java heap size when running Java tools)', subcategory='platform'))
+ self.sate.add_option('max_mem_mb', IntUserSetting(name='max_mem_mb', default=1024, min=1024, max=None, short_name=None, help='The maximum memory available (for the Java heap size when running Java tools)', subcategory='platform'))
self.sate.add_option('aligner', StringUserSetting(name='aligner', default='mafft', short_name=None, help='The name of the alignment program to use for subproblems.', subcategory='tools'))
- self.sate.add_option('merger', StringUserSetting(name='merger', default='opal', short_name=None, help='The name of the alignment program to use to merge subproblems.', subcategory='tools'))
+ self.sate.add_option('merger', StringUserSetting(name='merger', default='muscle', short_name=None, help='The name of the alignment program to use to merge subproblems.', subcategory='tools'))
self.sate.add_option('tree_estimator', StringUserSetting(name='tree_estimator', default='fasttree', short_name=None, help='The name of the tree inference program to use to find trees on fixed alignments.', subcategory='tools'))
self.sate.add_option('break_strategy', ChoiceUserSetting(name='break_strategy', default='longest', choices=['centroid', 'longest'], multiple_choices=True, short_name=None, help='The method for choosing an edge when bisecting the tree during decomposition', subcategory='decomposition'))
self.sate.add_option('max_subproblem_size', IntUserSetting(name='max_subproblem_size', default=3, min=0, max=None, short_name=None, help='The maximum size (number of leaves) of subproblems. When a subproblem contains this number of leaves (or fewer), then it will not be decomposed further.', subcategory='decomposition'))
View
16 sate_ui.xml
@@ -27,15 +27,21 @@
<string-option name="model" default="" category="raxml">
<help>Substitution model used by RAxML.</help>
</string-option>
+ <infile-option name="args" default="" category="raxml">
+ <help>Arguments to be passed to RAxML.</help>
+ </infile-option>
<infile-option name="path" default="" category="fasttree">
<help>Path to FastTree</help>
</infile-option>
<string-option name="model" default="" category="fasttree">
<help>Substitution model used by FastTree.</help>
</string-option>
- <string-option name="options" default="" category="fasttree">
- <help>Options to be passed to FastTree.</help>
- </string-option>
+ <infile-option name="options" default="" category="fasttree">
+ <help>Options to be passed to FastTree (equivalent of args).</help>
+ </infile-option>
+ <infile-option name="args" default="" category="fasttree">
+ <help>Arguments to be passed to FastTree.</help>
+ </infile-option>
<infile-option name="path" default="" category="opal">
<help>Path to Opal jar file</help>
</infile-option>
@@ -104,13 +110,13 @@
<int-option name="num_cpus" default="1" min="1" category="sate" subcategory="platform" must-be-valid="True">
<help>The number of processing cores that you would like to assign to SATe. This number should not exceed the number of cores on your machine.</help>
</int-option>
- <int-option name="max_mem_mb" default="2048" min="1024" category="sate" subcategory="platform" must-be-valid="True">
+ <int-option name="max_mem_mb" default="1024" min="1024" category="sate" subcategory="platform" must-be-valid="True">
<help>The maximum memory available (for the Java heap size when running Java tools)</help>
</int-option>
<string-option name="aligner" default="mafft" category="sate" subcategory="tools">
<help>The name of the alignment program to use for subproblems.</help>
</string-option>
- <string-option name="merger" default="opal" category="sate" subcategory="tools">
+ <string-option name="merger" default="muscle" category="sate" subcategory="tools">
<help>The name of the alignment program to use to merge subproblems.</help>
</string-option>
<string-option name="tree_estimator" default="fasttree" category="sate" subcategory="tools">

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