Installing GMOL

Installing GMOL

This article will guide you through the process of downloading and installing the GMOL application as well as downloading and extracting the sample data provided.

• Installing GMOL
• System Requirements
• Obtaining GMOL
• Starting GMOL
• Troubleshooting
  • Mac OS X
    • "gmol.jar" can't be opened because it is from an unidentified developer.
• Obtaining Sample Data
  • Downloading
  • Extracting

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System Requirements

• Java version 1.7 or higher
• Windows, Mac OS X, or Linux

Obtaining GMOL

To download the latest version of GMOL click here. The download contains an executable .jar file that will run on Windows, OS X, and Linux.

Starting GMOL

GMOL can be started in one of the following ways:

• Double-click gmol_1.0.jar file (Note: Your version number may be different.)
• Double-click on a created shortcut
• Click on a created Start menu entry
• From the command line (while in the directory containing gmol_1.0.jar) with: java -jar gmol_1.0.jar

Please see the troubleshooting section below if you have issues starting GMOL.

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Troubleshooting

Mac OS X

Common issues with installing GMOL on Mac OS X.

"gmol.jar" can't be opened because it is from an unidentified developer.

There are two ways to fix this error:

• Manually open using Jar Launcher
  1. Right-click on gmol_1.0.jar
  2. Select "Open With"
  3. Choose Jar Launcher
  4. A prompt will appear asking if you want to open it. Click "Open".

After opening GMOL once this way, you will be able to open it by simply double-clicking on gmol_1.0.jar in the future.

• Change security settings
  1. Go to "System Preferences" -> "Security and Privacy" -> "General"
  2. Click the unlock icon so that you can make changes.
  3. Choose the "Anywhere" option under "Allow apps to download from"

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Obtaining Sample Data

Provided separately from GMOL is a sample data set containing the human genome with sequence information. This data set is already in the .GSS file format required by GMOL so no conversion is needed.

*Note: Because the sample data set contains the entire human genome, the file is quite large. (Around 10GB once extracted) *

Downloading

To download the sample data provided click here. This will begin your download of a .zip file containing the data. Alternatively, you can click here to download the .zip archive directly from our servers.

Extracting

Once the data has finished downloading, extract it to a location of your choice. After extraction you should be left with a "human_with_seq" folder containing the data for each of the lower scales as pictured below.

Now that you have GMOL installed and the sample data properly extracted, you are ready to learn how to use GMOL with the walkthrough.