qiime2/paper2

paper2

development setup

The following is not necessary to run if you are following along with the tutorial. Only run these commands if you are publishing a new version or release of this document!

conda env create -n protocols --file qiime2-$RELEASE-py36-$ARCH-conda.yml
conda activate protocols
conda install -c conda-forge songbird redbiom -y
conda install -c bioconda bowtie2 -y
pip install https://github.com/knights-lab/SHOGUN/archive/v1.0.7.zip
pip install https://github.com/qiime2/q2-shogun/archive/master.zip
conda install cytoolz -y
conda install -c conda-forge sphinx awscli -y

building

export AWS_ACCESS_KEY_ID='MY_KEY_ID'
export AWS_SECRET_ACCESS_KEY='MY_SECRET_ACCESS_KEY'

make html

# once you have spot-checked the resulting HTML deploy the build:
make deploy

# and commit/push the latest `docs/` dir changes to this repo
git add docs/*
git commit -m "Some clever message here"
git push origin master

paper2's Issues

Songbird installation in conflict with QIIME 2 release 2021.8

Bug Description
Instructions for songbird installation on top of the latest QIIME 2 distribution cause errors. It appears the latest version of songbird is at odds with the QIIME 2 environment's Python version.

Steps to reproduce the behavior

1. Install QIIME 2 core distribution (release 2021.8) in conda virtual environment
2. Follow tutorial instructions to install songbird in the environment: conda install songbird -c conda-forge
3. See error screenshot below

Screenshots

Computation Environment

• OS: macOS Big Sur
• QIIME 2 Release 2021.8, in conda environment

--p-n-jobs should be renamed for qiime2-2021.8

Bug Description
The given command for computing diversity uses an outdated flag --p-n-jobs. The latest release of QIIME 2 (core 2021.8 distribution) renamed this to --p-n-jobs-or-threads.

Steps to reproduce this behavior

1. Follow the tutorial
2. Error out running qiime diversity core-metrics-phylogenetic, found twice in the alpha diversity section

BUG: metadata file from qiita is missing crucial columns

Bug Description
The metadata file in qiita must have been swapped since the last time these docs were built/tested.

The tutorial fails to run now because (most) metadata columns are missing. These are the only columns that I am finding right now in the file 81253_mapping_file.txt:
sample_name platform qiita_prep_id run_prefix

Steps to reproduce the behavior

1. Follow the tutorial
2. The moment you use the metadata file for anything, it fails on missing metadata columns

I am assuming that those columns were once present in the original metadata file, since this tutorial worked previously.

Including an automatic "Last Updated" date

Just wondering if it's possible to include an automatic "last updated" date at the top of manuscript following new builds/updates.
Possibly helpful:
https://github.com/mgeier/sphinx-last-updated-by-git/

Outdated link for reference seqs

Bug Description
In "Taxonomic classification" section the link to ref-seqs for training NaiveBayes classifier is not available anymore. It probably should be replaced by "https://github.com/BenKaehler/readytowear/raw/master/data/gg_13_8/515f-806r/ref-seqs.qza".

Steps to reproduce the behavior

1. Run

wget \
  -O "ref-seqs-v4.qza" \
  "https://github.com/BenKaehler/readytowear/raw/master/data/gg_13_8/515f-806r/ref-seqs-v4.qza"`

2. See ERROR 404: Not Found..