Running analyses on the server
The tools available on the different types of CLC Server are listed in CLC Genomics Server and Biomedical Genomics Server Extension.For more information on the tools, please see the manual for the workbench at http://www.qiagenbioinformatics.com/support/manuals/ or click the Help button in the dialogs that are shown when you run the tools.
When you run the analyses you will be faced with an initial dialog asking you where you wish the analysis to be run:
- Workbench. Run the analysis on the computer the CLC Workbench is running on.
- Server. Run the analysis using the CLC Server. For job node setups, analyses will be run on the job nodes.
- Grid. Submit the job to the CLC Server such that the job is then sent to be run on grid nodes.
Figure 2.4: Selecting where to run the analysis.
You can check the Remember setting and skip this step option if you wish to always use the selected option when submitting analyses. If you change your mind later on and want to switch, click Previous in the dialog when you start up an analysis. You will then be taken back to the dialog where you can choose where the analysis should be run.
Launching an analyses to run on a CLC Server, or on grid nodes, is identical to launching the same analyses to run on a Workbench, but there are three things to be aware of:
- You can only select data stored in locations configured on the server, with the exception of running data import. This means that when you are given the option to choose the data to use in an analysis, only server locations are shown. Further information about the exceptional case of data import is provided below.
- You have to save the result. For single analyses run on the Workbench, you can normally choose how to handle the results: Open or Save. Results from analyses performed on the server must be saved, so the option to open the results instead of saving them will be unavailable.
- When you click Finish, the analysis is submitted to the server to be handled. This means that you can close the Workbench or disconnect from the server without affecting the analysis. (See the notes on import below for an exception to this.) If an analysis has been completed when your Workbench is closed, or while it is not connected to the server, you will see a notification about this when you next log into the server from the Workbench.
Important note about data import to a server from a Workbench When using an import tool (Figure 2.5) you are offered the option of importing data from a local area, that is, an area accessible from the machine the CLC Workbench is running on, or from an area the CLC Server has access to. When importing data into the server from an area the CLC Server has access to, you can close your Workbench or disconnect it, right after submitting the job. However, when importing data from your local system to a server, the first part of the import involves uploading the data from the local system to the server system. During the upload phase, the Workbench must maintain its connection to the server. If you try to close the Workbench during this phase, you will see a warning dialog. You can see what stage tasks are at by opening the Processes tab in the lower left corner of the Workbench. Data upload from the Workbench to the server runs as a local process in the Processes tab. When the upload is done, a new process for the import is started. This will have a server icon. At this point, you can disconnect or close your Workbench without affecting the import.
Figure 2.5: Import tools are found under this menu in the Workbench.