Where can I get help?
This documentation is designed to walk users through the first stages of creating their research environments, and getting started in the environment. Capable users with some experience can be up and running in a handful of minutes - don't panic if it takes you a little more time, especially if you've not used Linux or HPC research environments before. Firstly - don't worry that you might break something complicated and expensive; one of the joys of having your own personal environment is that no one will tell you that you're doing it wrong, and nothing is at risk of being broken, aside from the data and work you've done yourself in the environment.
We encourage new users to run through a few tutorials in this documentation - even if you have plenty of HPC experience. Technology moves forward all the time and new features are constantly popping up that could save you effort in future. If you do run into problems, try replicating the steps you went through to get where you are - sometimes a typo in a command early-on in your workflow might not cause any errors until right at the end of your work. It can help to work collaboratively with other researchers running similar jobs - not only are two sets of eyes better than one, you'll both get something out of working together to achieve a shared goal.
For software application support you're going to need to contact the developers of the packages themselves. Remember that many of these software products are open-source and you've paid no fee to use them - try to make your bug-reports and enhancement requests as helpful and friendly as possible to the application developers. They've done you a great service by making their software available for you to use - please be respectful of their time and effort if you need to contact them, and remember to credit their software in your research publications.