# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1317828884 18000
# Node ID 4f797d3eee3abf3adb34be707ec8e1feea8ee44a
# Parent  370b3fc4e7d397adbba71220a194302f1dfe1fa2
Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS

diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/align.seqs.xml
--- a/mothur/tools/mothur/align.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/align.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -23,7 +23,7 @@
    --flip=true
    --threshold=$reverse.threshold
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/chimera.bellerophon.xml
--- a/mothur/tools/mothur/chimera.bellerophon.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/chimera.bellerophon.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -14,7 +14,7 @@
   #if int($increment.__str__) > 0:
    --increment=$increment
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/chimera.ccode.xml
--- a/mothur/tools/mothur/chimera.ccode.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/chimera.ccode.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -19,7 +19,7 @@
   #if int($numwanted.__str__) > 0:
    --numwanted=$numwanted
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/chimera.check.xml
--- a/mothur/tools/mothur/chimera.check.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/chimera.check.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -23,7 +23,7 @@
     --new_datasets='^(\S+)\.chimeracheck\.svg$:svg'
    #end if
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/chimera.pintail.xml
--- a/mothur/tools/mothur/chimera.pintail.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/chimera.pintail.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -33,7 +33,7 @@
    --increment=$increment
   #end if
   --result=#echo ','.join($results)
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/chimera.slayer.xml
--- a/mothur/tools/mothur/chimera.slayer.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/chimera.slayer.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -33,7 +33,7 @@
    $options.split
   #end if
   ## --blastlocation=path_to_blast
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/chimera.uchime.xml
--- a/mothur/tools/mothur/chimera.uchime.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/chimera.uchime.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -71,7 +71,7 @@
    #end if
   #end if
   $chimealns
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/classify.seqs.xml
--- a/mothur/tools/mothur/classify.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/classify.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -38,7 +38,7 @@
     --search=$classify.search.algorithm
    #end if
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/cluster.split.xml
--- a/mothur/tools/mothur/cluster.split.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/cluster.split.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -44,7 +44,7 @@
    --precision=$precision
   #end if
   $large
-  --processors=1
+  --processors=8
  </command>
  <inputs>
   <conditional name="splitby">
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/dist.seqs.xml
--- a/mothur/tools/mothur/dist.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/dist.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -16,7 +16,7 @@
   #if len($output.__str__) > 0:
    --output=$output
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/dist.shared.xml
--- a/mothur/tools/mothur/dist.shared.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/dist.shared.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -30,7 +30,7 @@
   #if $output.__str__ != "None" and len($output.__str__) > 0:
    --output=$output
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <!-- list,group  or shared -->
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/fastq.info.xml
--- a/mothur/tools/mothur/fastq.info.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/fastq.info.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -13,7 +13,7 @@
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta"/>
-  <data format="qual" name="out_qfile" label="${tool.name} on ${on_string}: qual"/>
+  <data format="qual454" name="out_qfile" label="${tool.name} on ${on_string}: qual"/>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/filter.seqs.xml
--- a/mothur/tools/mothur/filter.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/filter.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -30,7 +30,7 @@
   #if $hard.__str__ != "None" and len($hard.__str__) > 0:
    --hard=$hard
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/indicator.xml
--- a/mothur/tools/mothur/indicator.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/indicator.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -24,6 +24,7 @@
    --design=$design
   #end if
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.indicator.tre$:'$tree_out,'^\S+\.indicator.summary$:'$summary
+  --processors=8
  </command>
  <inputs>
   <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/metastats.xml
--- a/mothur/tools/mothur/metastats.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/metastats.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -26,7 +26,7 @@
   #if $sets.__str__ != "None" and len($sets.__str__) > 0:
    --sets=$sets
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/mothur_wrapper.py
--- a/mothur/tools/mothur/mothur_wrapper.py	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/mothur_wrapper.py	Wed Oct 05 10:34:44 2011 -0500
@@ -46,7 +46,7 @@
 
 debug = False
 #debug = True
-max_processors = 2
+max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
@@ -224,10 +224,10 @@
     cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
     cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']})
     cmd_dict['homova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
-    cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label']})
+    cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
     cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
     cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
-    cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] ,  'optional' : []})
+    cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] ,  'optional' : []})
     cmd_dict['make.group'] = dict({'required' : ['fasta','groups'],  'optional' : []})
     cmd_dict['make.shared'] = dict({'required' : ['list','group'],  'optional' : ['label','groups','ordergroup']})
     cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] ,  'optional' : ['method','iters']})
@@ -263,7 +263,7 @@
     cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
     cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
     cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']})
-    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']})
+    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast','processors']})
     cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
     cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
     cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name']})
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/pairwise.seqs.xml
--- a/mothur/tools/mothur/pairwise.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/pairwise.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -23,7 +23,7 @@
   #if len($output.__str__) > 0:
    --output=$output
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/parsimony.xml
--- a/mothur/tools/mothur/parsimony.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/parsimony.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -18,7 +18,7 @@
   #if int($iters.__str__) > 0:
    --iters=$iters
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/phylo.diversity.xml
--- a/mothur/tools/mothur/phylo.diversity.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/phylo.diversity.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -29,7 +29,7 @@
   #if len($rarefy.__str__) > 0 or len($collect.__str__) > 0:
    $summary
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <!-- list,group  or shared -->
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/rarefaction.single.xml
--- a/mothur/tools/mothur/rarefaction.single.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/rarefaction.single.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -33,7 +33,7 @@
   #if float($freq.__str__) > 0:
    --freq=$freq
   #end if
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/screen.seqs.xml
--- a/mothur/tools/mothur/screen.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/screen.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -51,7 +51,7 @@
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__]
   #end if
   --result=#echo ','.join($results)
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/summary.seqs.xml
--- a/mothur/tools/mothur/summary.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/summary.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -9,6 +9,7 @@
   #if $name.__str__ != "None" and len($name.__str__) > 0:
    --name=$name
   #end if
+ --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta,align" label="fasta - Dataset"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/summary.shared.xml
--- a/mothur/tools/mothur/summary.shared.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/summary.shared.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -19,6 +19,7 @@
   #end if
   $all
   $distance
+  --processors=8
  </command>
  <inputs>
   <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/trim.seqs.xml
--- a/mothur/tools/mothur/trim.seqs.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/trim.seqs.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -67,7 +67,7 @@
   #if $names.__str__ != "None" and len($names.__str__) > 0:
    --name=$names
   #end if
-
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
diff -r 370b3fc4e7d3 -r 4f797d3eee3a mothur/tools/mothur/unifrac.unweighted.xml
--- a/mothur/tools/mothur/unifrac.unweighted.xml	Tue Aug 09 11:39:27 2011 -0500
+++ b/mothur/tools/mothur/unifrac.unweighted.xml	Wed Oct 05 10:34:44 2011 -0500
@@ -23,7 +23,7 @@
    --distance=$distance
   #end if
   $root
-  --processors=2
+  --processors=8
  </command>
  <inputs>
   <!-- list,group  or shared -->