Changes

* replace the beginining ~/ with the actual path to where you downloaded gotcloud

* replace the beginining ~/ with the actual path to where you downloaded gotcloud

* replace ~/testalign with the directory where you want the test results to go

* replace ~/testalign with the directory where you want the test results to go

* To test the software in a cluster environment add the option -batchtype.

* To test the software in a cluster environment add the option -batchtype. For instance, using Sun Grid Engine in a Starcluster cluster, use

For instance, using Sun Grid Engine in a Starcluster cluster, use

  ~/gotcloud/gotcloud align --test ~/testalign -batchtype sgei

  ~/gotcloud/gotcloud align --test ~/testalign -batchtype sgei