Install/environment problems

[biodataganache]

Travis noted that he had issues with the mamba instructions and couldn't get things to work (ever). Conda seemed to work OK. Docker is fine (though we should definitely check this too to make sure).

For environment/install issues we should use VMs to test on a variety of platforms. I'm not 100% sure on what platforms/configurations we should check - or how we might fix problems when we find them (this seems very fussy) - but it's good practice to make sure users don't generally have problems with it.

[biodataganache]

See also #125

[jjacobson95]

I'll look into getting a new AWS birthright account. There are clean EC2 instances of linux, macos, ubuntu, windows (and more) that we could SSH into pretty easily to test. @christinehc you might want to as well if you don't already have one for the year (free for the project and I think we get $100 in credit).

Edit: Its $125 in credit and can be requested here: https://getcloud.pnl.gov/request/birthright

[jjacobson95]

We spoke about using pyenv recently, however based on my own difficulties getting pyenv to work, I'm going to suggest venv instead. venv is installed by default with python, is well supported, and is easy to use.

I haven't tested across multiple OS yet but this is what I'm doing locally:

Installation / Setup

# Get Repo requirements.txt file
git clone https://github.com/PNNL-CompBio/Snekmer.git
cd Snekmer
git checkout learn_decoy_implementation

# Install snekmer
python -m venv snekmer_venv1
source snekmer_venv1/bin/activate
pip install -r requirements.txt
pip install git+https://github.com/PNNL-CompBio/Snekmer.git@learn_decoy_implementation

[jjacobson95]

Just adding a note here to keep track / for debugging. The venv environment must be created in a directory without spaces in the path. i.e. this can't be built in something like /Users/jaco059/OneDrive - PNNL/Desktop/Snekmer.

So you can create / source the environment in home dir (~), then go run it wherever. But if it is created in a directory with spaces, it will mess up the file paths.

We will need to add this to the documentation.