BiQ Analyzer HiMod installation

BiQ Analyzer HiMod is a cross-platform application that runs on any operating system that has a recent version of Java Virtual Machine installed and properly configured. The tool requires Java SE Runtime Environment 7 or later (can be obtained from here).

For a typical run with up to several thousand sequences per analyzed reference BiQ Analyzer HiMod would need the system to have at least 2 Gb of operating memory. To support 2 Gb of operating memory, your Computer has to run a 64Bit Operating System. The program may process much larger sequences numbers but in this case the java heap space should be extended (see the Troubleshooting section below).

BiQ Analyzer HiMod is available either via Java Web Start (see Run BiQ Analyzer HiMod via Java Web Start) or as an interactive installer from IzPack (http://izpack.org/). The latter is supplied as an executable jar file (see Download BiQ Analyzer HiMod Installation package).

If you choose to use Java Web start, after clicking the "Launch" Button a jnlp file is downloaded to your harddisc. If it does not start the Application automatically, open the jnlp file by double clicking on it and it will download and start the BiQ Analyzer HiMod.

If you choose to download the installer, you have to extract the zip file downloaded to your harddisc and start the embedded jar file.
The first to see after starting the installer is a welcome page which gives some information about the team developing BiQ Analyzer HiMod. Click "Next" to proceed to a page showing information about the software itself. Proceed to the following step by clicking "Next" again and read and accept the licence agreement. In the next step you have to choose a installation path. Do so and proceed to a recap of the installation process. Another click on the "Next" button starts the installation. After it is finished, click "Next" one more time and after seeing a page telling you that the installation is finished you can leave the routine by clicking "Done".
Now you can start BiQ Analyzer HiMod by opening the folder you installed to and double-clicking "BiQ5HHT.jar".

Mac OS X Versions 10.7.5 and higher use by default a software called gatekeeper to prevent your Mac from malware. This software only allows to open software downloaded from the appstore or from "identified and trusted developers". If the BiQ Analyzer HiMod Installer or the installed BiQ HiMod won't open by double-click, you have bypass gatekeeper. There are different methods to do so. If you want to bypass gatekeeper for BiQ Analyzer 5 HHT only you have to open locate the jar file using the finder, right-click on it and select "open". In the appearing Popup you have to click "open" again to confirm. If you want to configure your Mac to open every software you download regardless where it's from, you can also reconfigure gatekeeper. Open "System Preferences / Security and Privacy" and choose the "General" tab. If everything is grayed out, click on the lock in the bottom left corner and type in your administrator password. This will allow you to make changes to your settings. Now you can change the "Allow applications downloaded from" option to "Anywhere". Note that the latter way of bypassing gatekeeper is only recommended for advanced users and is done on your own risk. (More information can be found here)

Windows may in some cases not set the java environment variable while installing java. If this is the case you can set this yourself to enable running BiQ Analyzer HiMod. The right value is based on where you have installed java. The default path is: "C:\Program Files\Java\[your java version]\bin". To set this variable follow the instructions given below.
Windows XP: Select Start, select Control Panel. Double click System, and select the Advanced tab. Click Environment Variables. In the section System Variables, find the PATH environment variable and select it. Click Edit. If the PATH environment variable does not exist, click New. In the Edit System Variable (or New System Variable) window, specify the value of the PATH environment variable. Click OK. Close all remaining windows by clicking OK.
Windows Vista: From the desktop, right click the My Computer icon. Choose Properties from the context menu. Click the Advanced tab (Advanced system settings link in Vista). Click Environment Variables. In the section System Variables, find the PATH environment variable and select it. Click Edit. If the PATH environment variable does not exist, click New. In the Edit System Variable (or New System Variable) window, specify the value of the PATH environment variable. Click OK. Close all remaining windows by clicking OK.
Windows 7: From the desktop, right click the Computer icon. Choose Properties from the context menu. Click the Advanced system settings link. Click Environment Variables. In the section System Variables, find the PATH environment variable and select it. Click Edit. If the PATH environment variable does not exist, click New. In the Edit System Variable (or New System Variable) window, specify the value of the PATH environment variable. Click OK. Close all remaining windows by clicking OK.
Windows 8: Run Control Panel in Windows 8's Metro UI Click More Settings in Control... on the left. Search "Environment Variables" in Control Panel, and click "Edit the system environment variables". Click on "Environment Variables..." Scroll down to highligh and edit path items. Add your path in the path string. Click OK to finish.