BasePlayer

User Guide

Open the online manual
Read the protocol at Nature Protocols

You can post your questions to our support forum at groups.google.com

Make sure you have Java jre 1.8 or newer installed. Note: OpenJDK "9-Ubuntu" has issues with autoupdate.
BasePlayer can be updated automatically at "File > Update" or manually by downloading BasePlayer.jar from https://baseplayer.fi/update/
Download the BasePlayer and unzip/install it to any location with enough hard-disk space (e.g. in the human studies, the reference genome size is ~3GB)
When using "BasePlayer portable package", click Launcher.jar (in unix you need jar-launcher and Launcher.jar must have executable rights.) Alternatively click BasePlayer.jar (may not allocate enough memory for the software)
Start the software with the BasePlayer launcher file (e.g. BasePlayer.exe) if you have used the installer.
If nothing happens, go to console/shell/command prompt and to your BasePlayer directory. Type: java -Xmx1200m -jar BasePlayer.jar
Download preferred reference genome from the genome selection menu, which appears on the first start.
You can allocate more memory for BasePlayer by editing the baseplayer_config.txt file in your home directory. e.g. MemoryLimit=1200m -> MemoryLimit=4G. Use Launcher.jar to apply the change.
Use BasePlayer.vmoptions file in the BasePlayer directory for memory allocation if installer is used

Basic navigation tutorial can be viewed here