Installation

BiQ Analyzer 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 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).

BiQ Analyzer is available for the major OS (Windows, Linux, MacOS). For Windows and Linux the preferred installation method is via an interactive installer from IzPack (http://izpack.org/). The latter is supplied as an executable jar file.

IzPack installer is functional on all supported platforms, including MacOS. However the system integration on Mac OS X is implemented insufficiently at the moment. Therefore we offer both tools also as standard MacOS applications packaged in a single Apple disk image (dmg).

If you choose to download the installer, you have to extract the downloaded zip file downloaded and start the embedded jar file. On most systems a double-click should work provided that Java Runtime was correctlyl installed and configured. In case it does not help, the context (righ-button) menu should contain a necessary record either in the main list of items or in the "Open with..." sub-menu. Finally, the installer can be started in the command line using the command "java -jar install_BiQ_Analyzer.jar" executed in the directory where the downloaded zip package has been extracted.

The installation starts with a welcome page which gives some basic information about BiQ Analyzer. Click "Next" to proceed to a page mode detailed description of the installed software. Proceed to the following step by clicking "Next" one more time, read and accept the licence agreement. In the next step you have to choose an installation path. The installer should normally be started with Administrator privileges and you should be able to specify any existing path (e.g. C:\Program Files directory on Windows). In case you want the package to be installed to an alternative location, specify it and proceed to a recap of the installation process. Another click on the "Next" button starts the installation process itself. After the latter is finished, click "Next" one more time and after seeing a page with a confirmation you can leave the routine by clicking "Done".

After successful installation the BiQ Analyzer program group should appear in the system application menu (e.g. the "Start" menu/surface in Windows). There will be separate shortcuts in the group for starting BiQ Analyzer HiMod and BiQ Analyzer 3 "Classic". On Windows platforms three more shortcuts will be added: two shortcuts to start both tools with a system terminal to monitor the error messages, and the uninstaller shortcut.

In case the system integration did no work properly, and the shortcuts were not generated you can start BiQ Analyzer by opening the folder you installed to and double-clicking one of the start scripts, most of which have self explanatory names, e.g. "start_BiQ_Analyzer_3_win.bat" to launch "Classic" BiQ Analyzer on Windows or "start_BiQ_Analyzer_unix.sh" to start BiQ HiMod on a Unix-compatible system.

Installation of the MacOS X Application bundles is as simple as usual in this case. After downloading and mounting the dmg file open the mounted volume with the Finder application. To install drag and drop one of or both BiQ Analyzer 3 and BiQ Analyzer HiMod to the "Applications" bookmark in the left pane of the Finder. After the completion of teh copying process the application(s) should appear in the Launchpad.

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 Installer or the installed BiQ 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 about the Gatekeeper 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. 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 highlight and edit path items. Add your path in the path string. Click OK to finish.