Dear participants of the PASTA tutorial,

I am glad you will be joining us for this session and I hope to make it a good use of everybody's time. To that end, it would be helpful if everybody attending could install PASTA in advance of the session. Detailed installation instructions can be found at https://github.com/smirarab/pasta, although I have included a summary and a couple pointers to go along with those instructions at the bottom of this note.

Please feel free to contact me at nute2@illinois.edu if you have any problems during the installation process. I will be in Austin on Wednesday afternoon and would be happy to help debug if people have issues during installation.

Thank you, and please check out the pointers below before jumping right into the instructions, especially if you don't install software manually very often. See you all on Friday!

Regards,

Mike Nute

Summary:

There are three options for installing PASTA: 1) installing directly from source (Mac & Linux only), 2) Installing the pre-built Mac image (dmg) file (Mac only), and 3) using the pre-built virtual machine (Mac, Linux & Windows). Unfortunately for Windows the last method is currently the only option. Download links for the last two are provided in the instructions. The pre-built Mac image option, for mac users, is simple and well-explained in the instructions. For non-Mac users:

Installing from Source:

For Linux users, this is probably the easiest option. For MAC users comfortable with installing from source, it might be.

Take note of the dependencies listed, particularly Java and wxPython. Python comes packaged with most Linux distributions, and dendropy is automatically installed if it has not been already. But WxPython is required to run the GUI, which will be the focus of the tutorial, and must be installed manually. On Ubuntu, some simple commands to take care of these dependencies before going to step 1 are:

• sudo apt-get install default-jre
• sudo apt-get install python-wxgtk3.0
• sudo apt install python-pip
• sudo apt install git

It is ideal to follow steps 1-3 closely so that the directory structure has the cloned "pasta" and "sate-tools-***" folders side-by-side under some specified install folder. If you have installed PASTA from source, it is a good idea to test it and make sure no errors arise. To do this, navigate to the main install folder (just above the folders created by the git clone operations) and run the following, which should run in just a few minutes:

• mkdir ./temps; python ./pasta/run_pasta.py -i ./pasta/data/small.fasta -o ./pastajob --temporaries=./temps

Using the Virtual Machine (WINDOWS users)

If you are experienced and comfortable with Virtual Machines, this is by far the option with the fewest steps. The virtual appliance given in the instructions is ready to be run from various virtualization software, including VirtualBox, which we use.

Note that the VM file is 2.5Gb, so please try to download it in advance of the session.

If you are not experienced with Virtual Machines, you will need to enable virtualization within your BIOS and install VirtualBox.

• To edit your BIOS, on your typical Windows machine you will have to re-boot the computer, and somewhere in the first few seconds there is an option to hold one of the "F"-keys to enter the BIOS menu (google this in advance). This will lead you to a small set of menus you will navigate with the keyboard, one of these menus or sub-menus should pertain to virtualization, and there should be one option to "enable virtualization" or something to that effect, which will be disabled by default. Enable that, and if there are others related to virtualization that look like they could be enabled, you may want to enable those too. Enabling virtualization will not harm your computer or hurt its performance. After you've enabled those, navigate your way out of the BIOS menu, saving any changes along the way.
  NOTE: This may sound like a lot of work and like a goose chase for the right option, but it's really not at all. Here is an example of what the BIOS menu on my computer looks like that I just put together: http://publish.illinois.edu/michaelnute/bios-menu/
• VirtualBox is a free software (made by Oracle) and a great utility for running Linux on a PC. There is a link in the instructions but a simple google search will lead you through the download and install process.

After you follow the instructions above, download the virtual appliance and import it into VirtualBox, you'll have to decide how many processors and how much RAM to allow it to use. I tend to let it have all the processors and all but about 4 gigs of my RAM. It won't use these unless it needs them, so there's not much downside to erring higher.

If you are running VirtualBox on Windows, once you have installed it and gotten the machine running, I strongly recommend installing the VirtualBox Windows Guest Additions for that machine, which make the user experience much nicer. Instructions for those are here: https://www.virtualbox.org/manual/ch04.html

If you have this up and running ok, it may not be strictly necessary to test it but it's never a bad idea. To test it, open a terminal (from the icon in the left-hand column) and run the following command, which should run in just a few minutes:

• python ~/tools/pasta/run_pasta.py -i ~/tools/pasta/data/small.fasta -o ~/pastajob --temporaries=~/temp

Finally, a best-practice when using VirtualBox is to set up shared folders between the virtual machine and your hard drive and work mostly in those shared folders. This has some quirks but it makes life a lot easier and avoids letting the VM hard drive grow out of control. Those can be set up in the settings for the VM but they have to be mounted manually every time the VM is started, so it's good to have a startup script to do this automatically.