New to Qiime and have questions on setting up and installing Qiime on Ubuntu 16.04 in vSphere v6.7

[Christopher M Miller]

Hello, I am a Linux System Admin and I work in a research facility where a few doctors, scientists and researchers have reached out to me to setup Qiime on Ubuntu 16.04 in VMWare vSphere.  They want to have two Ubuntu VMs, one with Qiime v1 and the other with Qiime v2.  Most of them want to do their work on the VM with Qiime v1, since they are very familiar with that version and start to learn more about Qiime v2 with the other VM. 

I don't know much about the software and I've been reading this Google Group along with the website and I have a few questions, in the hopes of getting the setup correct. 

- When I build, I like to optimize the VM to the best of my ability.  Looks like I can allocate one data disc in vSphere to host the Ubuntu VM.  Will this be ok?  The people that I'm supporting are asking for 1 TB size VMs as they are processing very large samples (I think this is the correct term).

- I will use paravirtual scsi adapters for connections, unless others have other recommendations. 

- I want to setup multiple partitions in the Ubuntu VM, such as /var, /var/tmp/, /tmp, /opt, /home, and /usr/local.  Will this cause an issue or are there recommendation partitions with working with Qiime?

- Looks like Qiime doesn't use a daemon, but reminds me of python pip.  Where from a Bash Shell prompt, the end user can type "qiime" and it changes the prompt to show 'qiime" and they can start their work with the software.  From shadowing these users looks like do most of the software work from their home directory.  Should I allocate more space to /home directories due to this? 

Hope these questions are clear and thanks in advance.

- Chris

[Colin Brislawn]

Hello Chris,

Thank you for your detailed post. Let me see how I can help.

I know this is stating the obvious after the banners at the top of this forum, but Qiime 1 is no longer supported. Qiime 2 is supported very well by the developers, and now is the perfect time to switch to Qiime 2. There is extensive documentation about setting up Qiime 2 vms over here: https://docs.qiime2.org/2018.8/install/virtual/virtualbox/ 

Now let's talk about the architecture of Qiime 1. You are correct that qiime doesn't have a daemon; qiime 1 is literally just a bunch of python scripts that connect unix CLI programs. So researchers are just running these scripts from their home directory, and these scripts are in turn calling programs like vsearch. 

We distribute both Qiime 1 and Qiime 2 inside conda virtual environments (which are basically like virtualenvs in python). You could easily install both Qiime 1 and Qiime 2 into two different conva environments on the same VM, if you wanted to. Full install instructions are over here: 

http://qiime.org/install/install.html 

(Part of the reason I'm recommended conda is that manages dependances of Qiime. While Qiime itself is pure python, it depends on boatloads of software, so deploying it all using conda is really elegant.) 

the end user can type "qiime" and it changes the prompt to show 'qiime" and they can start their work with the software

Looks like they are using an older version of qiime ;-) When using a conda environment, they would type

source activate qiime1

then just run the python script directly. 

Disk space: 1T of disk should be good to start. Some analysis steps are very RAM heavy, so having at least 16 GB of memory would be a good start. I'm sure you can allocate more memory if needed.

Directories: I think some qiime scripts need /tmp/ as a temporary directory, but most scripts can use any input and output you list. 

Let me know if this helps,

Colin