-How To add a new executable\r
-\r
-1) Add executable to the binaries folder. If it has source code and can be recompiled for different platforms include it under binaries/src \r
-Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. \r
-\r
-2) Make sure all the dependencies of the software being installed are satisfied. If there are other binaries they should be included as well. Keep the dependant binaries in subfolder for the main executable. Update compily and setexecflag scripts accordigly. \r
-\r
-3) Make sure executable \r
- - 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
+How To add a new executable.\r
+\r
+1) Add executable to the binaries folder. If it has source code and can be\r
+ recompiled for different platforms include it under binaries/src \r
+ Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. \r
+\r
+2) Make sure all the dependencies of the software being installed are satisfied. \r
+ If there are other binaries they should be included as well. Keep the dependant \r
+ binaries in subfolder for the main executable. Update compile and setexecflag \r
+ scripts accordingly. \r
+\r
+3) Make sure executable does not have any hard links to its dependencies, e.g. \r
+ is able to run from any installation folder and does not contain any hard \r
+ coded paths. (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 \r
+ for 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