sourcetracker2 plugin?

Community Plugin Support
1

Hi there!

I was trying to use sourcetracker2 with my QIIME2 feature table. I’m having some issues with the biom file I exported from qiime in the sourcetracker2 package from github, and I see some evidence that there is (was?) a q2-sourcetracker plugin. I thought I’d try and see if I could utilize the qiime plug in if it exists, to make the process simpler… however it looks like the q2 package is gone? Or I’m just looking in the wrong places!

Anyway, I’m just wondering if a q2-sourcetracker2 plug in still exists.

Thanks!
Claire

4

Hi @clairewill22 ,
It looks like the plugin is installed as part of the main package: GitHub - biota/sourcetracker2: SourceTracker2

but I do not see usage instructions. You could just try installing that package, refresh QIIME 2, and :pray:

@cmartino it looks like you were involved in developing the Q2 plugin for sourcetracker2… could you please advise us on how to install and use the plugin? Thanks!

1 Like
5

Hi @clairewill22 and @Nicholas_Bokulich,

It looks pypi has not caught up with the master of sourcetracker2. There was also an error on the install with the citations.bib not tracking. I just put in a PR to their master repo with a fix for that. In the meantime, if you want to just use my bug fixed branch for now you can install it by running:

pip install git+https://github.com/cameronmartino/sourcetracker2@fixq2citations

and then

qiime dev refresh-cache

There is a tutorial here on using st2 with QIIME2.

I will also note that I also made a Q2 plugin for FEAST that is here (PR is here). You can install that by first installing FEAST.

conda install -c bioconda -c conda-forge -c r bioconductor-phyloseq r-devtools r-magrittr r-dplyr r-vgam r-tidyr r-vegan r-reshape2 r-rcpp r-rcpparmadillo r-gridextra r-ggplot2 r-ggthemes

> R
> devtools::install_github("cozygene/FEAST")
> quit()

running:

pip install git+https://github.com/cameronmartino/FEAST@FEAST_beta

then qiime dev refresh-cache

The tutorial for Q2-FEAST is here.

3 Likes
6

Thanks @cmartino ! When you get a chance, would you be interested in listing both of these in the QIIME 2 library? This would improve discoverability in the future. :grinning_face_with_smiling_eyes:

1 Like
7

@Nicholas_Bokulich,

Will do. :+1: I will ask the main authors to review/merge and push their new versions to pypi/cran. That way I am not giving wonky installs from git repos in the tutorials.

1 Like
8

Thanks, all!
This is great.
Best,
Claire

1 Like