[Bioperl-guts-l] bioperl commit

Juguang Xiao juguang at dev.open-bio.org
Fri Feb 14 05:18:54 EST 2003


Fri Feb 14 05:18:53 EST 2003
Update of /home/repository/bioperl/bioperl-pipeline/xml/templates/dev
In directory dev:/tmp/cvs-serv1799/templates/dev

Modified Files:
	juguang_debut_annotation.xml 
Log Message:
a simplifed xml after the converter innovation.

bioperl-pipeline/xml/templates/dev juguang_debut_annotation.xml,1.1,1.2
===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/xml/templates/dev/juguang_debut_annotation.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /tmp/T0IRaOId	2003-02-14 05:18:54.050000909 -0500
+++ /tmp/T1JRaOId	2003-02-14 05:18:54.060004435 -0500
@@ -97,14 +97,9 @@
 
    <converter id="1" module="FeaturePairToEnsEMBLConverter">
       <method name="new" rank="1">
-         <argument tag = "-host" value = "mysql"/>
-         <argument tag = "-driver" value = "mysql"/>
-         <argument tag = "-dbname" value = "juguang_homo_core_9_30"/>
-         <argument tag = "-user" value = "root"/>
          <!-- argument id = "15" tag = "-passwd" value = ""/ -->
          <!-- I think to make the analysis logic name build in the converter instance module, but gave up since that will decrease the flexibility. 
          -->
-         <argument tag="-analysis_logic_name" value="RepeatMask"/>
       </method >
       <method name="contig_name" rank="2">
          <argument value="INPUT" type="SCALAR" rank="1"/>
@@ -114,11 +109,6 @@
   <converter id="2" module="HSPToEnsEMBLConverter">
       <method name="new" rank="1">
          <argument tag = "-program" value = "blastx"/>
-         <argument tag = "-host" value ="mysql"/>
-         <argument tag = "-driver" value = "mysql"/>
-         <argument tag = "-dbname" value = "juguang_homo_core_9_30"/>
-         <argument tag = "-user" value = "root"/>
-         <argument tag="-analysis_logic_name" value="blastall"/>
       </method >
       <method name="contig_name" rank="2">
          <argument value="INPUT" type="SCALAR" rank="1"/>
@@ -151,12 +141,9 @@
 		<logic_name>RepeatMasker</logic_name>
 		<runnable>Bio::Pipeline::Runnable::RepeatMasker</runnable>
 		<program>RepeatMasker</program>
-		<nodegroup_id>1</nodegroup_id>
 		<analysis_parameters>-lib all.lib</analysis_parameters>
-			
 		<input_iohandler_mapping current="" next=""/>
 		<output_iohandler id="3" converter_id="1" />
-			
 	</analysis>
 	
 	<analysis id="3">



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