Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

[jabaws.git] / conf / settings / JpredPresets.xml

diff --git a/conf/settings/JpredPresets.xml b/conf/settings/JpredPresets.xml
index 5407708..c70e709 100644 (file)
--- a/conf/settings/JpredPresets.xml
+++ b/conf/settings/JpredPresets.xml
@@ -3,26 +3,12 @@
     <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>\r
 \r
     <preset>\r
-        <name>cluser-single</name>\r
+        <name>cluser-configuration</name>\r
         <description>\r
             Dundee cluser configuration for single sequence prediction\r
         </description>\r
         <optlist>\r
                        <option>-dbpath /homes/www-jpred/databases </option>\r
-                       <option>-dbname uniref90</option>\r
-                       <option>-jabaws</option>\r
-                       <option>-seq</option>\r
-        </optlist>\r
-    </preset>\r
-\r
-    <preset>\r
-        <name>cluster-alignment</name>\r
-        <description>\r
-            Dundee cluser configuration for multiple sequence alignment prediction\r
-        </description>\r
-        <optlist>\r
-                       <option>-dbpath /homes/www-jpred/databases </option>\r
-                       <option>-dbname uniref90</option>\r
                        <option>-jabaws</option>\r
         </optlist>\r
     </preset>\r
@@ -30,26 +16,11 @@
     <preset>\r
         <name>single</name>\r
         <description>\r
-            4-core laptop configuration for single sequence prediction\r
-        </description>\r
-        <optlist>\r
-            <option>-dbpath /data/UNIREFdb/</option>\r
-            <option>-dbname ported_db</option>\r
-            <option>-ncpu 3</option>\r
-            <option>-jabaws</option>\r
-            <option>-seq</option>\r
-        </optlist>\r
-    </preset>\r
-\r
-    <preset>\r
-        <name>alignemnt</name>\r
-        <description>\r
-            4-core laptop configuration for multiple sequence alignment prediction\r
+            4-core computer configuration for single sequence prediction\r
         </description>\r
         <optlist>\r
             <option>-dbpath /data/UNIREFdb/</option>\r
-            <option>-dbname ported_db</option>\r
-            <option>-ncpu 3</option>\r
+            <option>-ncpu 4</option>\r
             <option>-jabaws</option>\r
         </optlist>\r
     </preset>\r