Adding QIIME2 plugin into FEAST_beta#8
Open
cameronmartino wants to merge 75 commits intocozygene:FEAST_betafrom
Open
Adding QIIME2 plugin into FEAST_beta#8cameronmartino wants to merge 75 commits intocozygene:FEAST_betafrom
cameronmartino wants to merge 75 commits intocozygene:FEAST_betafrom
Conversation
…into FEAST_beta
Author
|
A visualization of the mixing proportions is now included with the QIIME 2 plugin through a FEAST specific barplot function. Although it produces a single stacked bar plot -- it can be split into multiple using the
|
Since the file isn't actually structured like a .qza, trying to load it in view.qiime2.org causes that site to explode :) ... naming it like a .tsv is more accurate and hopefully less confusing to users
The presence of these files caused installation errors when installing the FEAST R package from source on a Linux system a few weeks back. My assumption is that these files were built for another system (probably MacOS since leaving these files in during installation seemed to work fine on the Mac system I'm currently using), so removing them (thus forcing recompilation) should make this more cross-platform. Or, uh, something like that. Thanks @gwarmstrong for figuring this out a few weeks back :)
some stuff assumed there was a folder called "q2_FEAST", but it's actually named q2_feast. This doesn't seem to cause problems on mac systems, but it broke the tests on a linux system -- likely due to ways the diff operating systems handle case sensitivity in file/folder names.
Also added some documentation to the top of setup.py explaining a few things about q2-FEAST's installation process. Hopefully the ramblings are helpful ;)
mostly did this so i don't forget this a few months down the line, but might be useful to other folks
Address Linux installation problems, add developer documentation, other small tweaks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This provides a QIIME2 plugin for the existing FEAST script. This includes tests and a pip installation.
There are multiple inputs:
These inputs can definitely be optimized for easier use in the future but this provides a functional solution for now.