Running tools

Launching tools and workflows involves the same series of general actions:

There are several ways to launch a tool or installed workflow:

Using the Quick Launch tool to start jobs

The Quick Launch tool, shown in figure 10.1, is started by clicking on the Launch button (Image launch_16_n_p) in the toolbar. It can also be launched using the keyboard shortcut Ctrl + Shift + T (Image command_key_web + Shift + T on Mac), or by going to the Toolbox menu at the top of the Workbench and selecting the top option, Launch (Image launch_16_n_p).

Image quicklaunch-genomics
Figure 10.1: Tools and installed workflows can be quickly found and launched using the Quick Launch tool.

In the Quick Launch dialog, you can type terms in the text field at the top. This will filter for tools and installed workflows with matches to these terms in the name, description or Toolbox location. For tools where names have been changed between Workbench versions, searches using old names will still filter for the relevant tool. Using single or double quotes (' or ") will find a literal quote of the searched term.

In the example shown in figure 10.2, typing create shows a list of tools involving the word create. The arrow keys or mouse can be used for selecting and starting a tool from this list.

Image quicklaunch-typing-genomics
Figure 10.2: Typing in the search field at the top will filter the list of tools to launch.

Click on the Favorites tab to see the subset of tools that are frequently used, or have been selected as favorites. See Favorites tab for further details.

Configuring and submitting jobs

When you open a tool or installed workflow, a wizard pops up in the center of the View Area. Stepping through a succession of wizard steps, you will select the data to analyze, configure any analysis parameters, and specify how the results should be handled. You can navigate between wizard steps by clicking the buttons Next and Previous at the bottom of the window.

If you have logged into a CLC Server from your Workbench, you will first be asked to select whether the job should be run on the Workbench or submitted to the server. These choices, along with information about data selection and other considerations when launching tasks on a CLC Server are provided in Running a tool on a CLC Server.

Generally, the first analysis configuration step involves selecting the data elements to be used as input. A view of your Navigation Area will be presented to you. That view will show data elements appropriate for use as input for that tool. Folders are also shown. For example, in figure 10.3 you can see a the Workbench Navigation Area (on the left) and a view of the same Navigation Area in the wizard (on top) for the Assemble Sequences tool. This tool only accepts nucleotide sequences and nucleotide sequence lists, so data elements of other types that can be seen in the Workbench Navigation Area, such as the one called "Read mapping", and the amino acid sequence ATP8a1, are not displayed in the wizard Navigation Area.

The data types that can be used as input for a given tool are described in the manual section about that tool. This documentation can be opened directly by clicking on the Help button in the bottom left corner of the launch wizard.

Image runjob1
Figure 10.3: You can select input files for the tool from the Navigation Area view presented on the left hand side of the wizard window.

To indicate the data elements to be used in the analysis, either double click on them in the "Navigation Area" view on the left, or select them with a single click and then click on the right hand arrow. These items will then be listed in the "Selected elements" list on the right. If data elements of appropriate types were already selected in the Workbench Navigation Area before launching the tool, these will be automatically entered into the Selected elements list. To remove entries in that list, just double click on them or select them with a single click and then click on the left hand arrow.

When multiple elements are selected, most analysis tools will treat all those elements as a single input data set unless the "Batch" option at the bottom, has been selected. If that option is selected, then the tool will be run multiple times, once for each "batch unit", which may be a data element, or folder containing data elements or containing folders of elements. Batch processing is described in more detail in Batch processing.

Once the data of interest has been selected, click on Next. Depending on the tool, there may now be one or more steps for configuring analysis parameters. An example is shown in figure 10.4. Clicking on the Reset button resets all parameters in that step to their default values.

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Figure 10.4: An example of a "Set parameters" window.