- - Does not have any hard links to its dependencies, e.g. is able to run from any installation folder and does not contain any hardcoded paths. (TODO examples...) \r
-\r
-4) Describe executable in conf/Exectuable.properties. \r
-\r
-5) Add <ExecutableName>Limit.xml, <ExecutableName>Parameters.xml and <ExecutableName>Presets.xml. All but Limits are optional. \r
-\r
-6) Create a Java wrapper class for your executable. Create it within runner source directory.\r
+ - Does not have any hard links to its dependencies, e.g. is able to run from \r
+ any installation folder and does not contain any hard coded paths. \r
+ (TODO examples...) \r
+\r
+4) Describe executable in conf/Exectuable.properties. The lowercase name of the \r
+wrapper should be included in the name of the property for example Clustal \r
+properties all include clustal as a part of the name e.g. local.clustalw.bin\r
+The same property for Mafft will be called local.mafft.bin. \r
+\r
+5) Add <ExecutableName>Limit.xml, <ExecutableName>Parameters.xml and \r
+<ExecutableName>Presets.xml. All are optional (should be at least). If the \r
+executable does not support parameters you do not have to refer to the \r
+XXXParameter.xml file into the Executable.properties file. The same is true for \r
+Presets and Limits. \r
+\r
+6) Create a Java wrapper class for your executable. Create it within runner \r
+source directory. Examples of other wrappers can be found in compbio.runner.msa \r
+or compbio.runner.disorder packages. Wrapper should extend SkeletalExecutable<T> \r
+implements PipedExecutable<T> if you need to pass the input or collect the \r
+results from the standard in/out. Please see Mafft code as example. Wrapper \r
+should expend SkeletalExecutable<T> if input/output can be set as a parameter \r
+for an executable. Please see ClustalW code as example. \r