Setting up the Qiime VM

Goal: Get Qiime running the the VirtualBox and fine-tune its settings.

Methods: The Qiime pipeline is distributed as a Virtual Machine (VM). This way, the complex pipeline 'just works.' At least that's the hope. These are the steps I took while setting up Qiime 1.7.0.

Installing the Qiime Virtual Box is very well documented. I followed those steps. Because I'm on Windows, I used 7-zip to open the compressed .gz file. Everything else is the same.

After following these instructions, I opened the Virtual Machine (VM) to make sure it was working. I also did the following things.

1. Installed the VirtualBox Guest Additions using the disk icon on the left side of the screen.
2. Installed the Synaptic Package Manager using the Ubuntu Software Center.*
3. Installed the package 'nautilus-open-terminal'*
4. Installed these packages: ipython, ipython-notebook-common, and ipython-notebook
5. Did updates (all of them, I think... In Qiime 1.6.0, some updates caused problems. I don't remember any problems in Qiime 1.7.0)*
6. Changed some Settings: (first, I shut down the VM)
1. Gave my VM access to more memory and processor cores. (in settings>system)
2. Made Shared Clipboard and Drag'n'Drop bidirectional (settings>general>advanced)*
3. Connected the Shared_Folder on my virtual desktop, to a folder in my real computer. (settings>Shared Folders>Add Shared Folder)
7. Pinned Synaptic Package Manager, System Monitor, and Files to my Dashboard.*
8. Opened Terminal and ran the script 'print_qiime_config.py' (And it worked!)

*Yeah, you don't really need to do these steps. I find these programs useful and convenient, but they are not strictly needed.

4 hours