Executing a Tool

If you go to the Tools page, you will see the Available Tools list in the left panel. You can run any of these tools. If you're registered and signed into the BioExtract Server and have added tools to your workspace, you will also see a My Tools group in the list.

The basic steps for executing tools are:
Step 1. Select a tool
Step 2. Input some data
Step 3. Define parameters
Step 4. Click Execute and wait
Step 5. View tool results

Step 1. Select a tool

From the Tools page, in the Available Tools list in the left panel, look through the tools for the one you need. For example, click Similarity Search Tools (click on the name or the plus sign) and you're offered: blastn, blastp, blastx, tblastn and tblastx.

When you find the tool you need, click on its name. The tool’s form will open in the right panel. You’ll use this form to get more information about the tool, to input your data, to define parameters and to view tool results.

Step 2. Input some data

Go to the Input Data section near the top of the tool form. BioExtract Server offers four different ways to input data:

Error from tools

Make sure the entered data matches the format requirements of the selected tool. To get information about a tool's format requirements, click More Information at the top of the tool form. A window to tool help will open. Check format requirements. If there is a format mismatch, you can use BioExtract Server's FormatConversion tool to correct the issue. Read How to convert between different file formats.

Step 3. Define parameters

Go to the Parameter Settings section. You can keep the parameter settings at their defaults or change them according to your data and preferences.

If you need help with parameters, click the More Information link at the top of the tool form. A window to tool help will open.

Step 4. Click Execute and wait

Click the Execute button at the bottom of the tool form. The button will change to read Terminate and a status message will appear just below it. Now wait. Do not leave the Tools page while waiting. Leaving will stop tool execution. After successful completion, the status message will read Execution Complete.

If you want to stop execution, click Terminate. The status message will change to Terminated, and the tool will stop.

Step 5. View tool results

Tool results can be found in the Tool Results drop–down menu at the bottom of the tool form. To view tool results, open this menu, select a file of interest and then click View Results. A new window will open with the results. Result files may be viewed, downloaded and used as input into subsequently executed analytic tools.

Other important information