Update readme to mention the github releases

[jspaezp]

Hello there!

First off, I am very impressed by the project so I wanted to make a minor contribution to the documentation. I added "installation" instructions for the pre-compiled binaries in the github releases.

In an additional effort to improve documentation:

• On the "notes" you also mention:

  • The majority of parameters are optional - only "database.fasta", "precursor_tol", and "fragment_tol" are required. Sage will try and use reasonable defaults for any parameters not supplied

  I am assuming that means reasonable for data-dependent narrow-window high-resolution ms2 runs, right? Should that be explicit?

• Should a page be added to explain all the features used internally for re-scoring?

• [x] Document the change in CLI that allows over-writting the json https://github.com/lazear/sage/pull/19

• [x] Document docker image usage (https://github.com/lazear/sage/pull/18) -> docker pull ghcr.io/lazear/sage:master

Thanks a lot for the great project! Sebastian

[lazear]

Hi Sebastian,

Thanks for the comments and PR - there should definitely be some effort to expand on the documentation!

1. Sure, we could add mention that Sage only supports DDA runs. I think most of the defaults are also reasonable for low-res MS2 scans as well, since precursor/fragment tolerances are required parameters - the other options controling database generation & spectral processing should largely be independent of MS2 resolution (tweaking them can lead to optimal searching however - e.g. turning on deisotoping for high-res scans).
2. If you'd like to get started on this, you can reference https://github.com/lazear/sage/blob/f5d065012dbd62f7cd8b01f020909d9f4db36b02/src/lda/mod.rs#L169-L188 and https://lazear.github.io/sage/#lda
3. & 4 I am also happy to merge in, if you provide! Perhaps we can utilize the GitHub wiki feature?

Thanks, Mike