There are a few common problems which can arise when running SeqMonk. Below are the most common things you are likely to see along with a work-round to get you going again.
SeqMonk is a java application. This means that in order to run SeqMonk you need to have installed a java runtime environment (JRE). If you do not have a JRE installed then SeqMonk will not start.
There are a number of free available JREs. SeqMonk has been tested to work with Oracle JREs v1.6 to v1.8 running under windows, linux and MacOSX. If you don't have this JRE already you can get it from http://java.sun.com. Other java environments/versions may also work, but we haven't tested them.
If you are on a Mac then rather than just the standard Java Runtime Environment (JRE) you need to have installed the Java Development Kit (JDK). Instructions for finding and installing this are in the INSTALL.txt document which you can view on the downloads page of the SeqMonk project website.
If SeqMonk starts to launch but the interface never appears then you should copy all of the debugging text which appears in your console and email it to the SeqMonk developers (or report it through out bug tracking system) and we will help you get things running.
The nature of the data SeqMonk has to deal with is that it is very large. Both genome annotations and sequence data take up huge amounts of memory. SeqMonk requires at least 2GB of RAM for small experiments, and large experiments will require more. If you're having problems with memory usage then look at the memory settings and preferences documentation to see how you can enable more memory or reduce the amount of memory SeqMonk requires.
If SeqMonk fails to import new genomes it's probably because it was unable to contact the web server which provides this data. In order to do this your machine needs to be able to access the internet.
If your machine is networked and genome importing still doesn't work then the most common cause is the proxy server settings (under Network from Edit > Preferences). If your network uses a proxy server you should enter its details here. If not then the proxy server name should be left blank.
If SeqMonk is ever closed without going through a normal shutdown process (eg crashing, or being killed in TaskManager) then it can leave behind cache files which will not be cleaned up. These won't prevent SeqMonk from running in the future, but they will take up space on your system and they serve no useful purpose. You will therefore be warned on startup if you have old temp files in your cache directory.
To clean up stale temp files simply close all instances of SeqMonk, then check in your cache directory and delete any file whose name starts with seqmonk and ends with .temp.
If you have two copies of SeqMonk running at the same time you will be incorrectly warned that you have stale temp files since the second copy will see the temp files from the first copy. In this case you can safely ignore this warning.