Set up a Qiime 2 environment - Gibbons-Lab/wiki GitHub Wiki

The steps here are very similar to the ones from the official tutorial with adjustments for our server.

Installation

Setup Qiime 2

You will need a Qiime 2 environment with version 2020.6 or higher (how to install Qiime 2).

wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml
conda env create -n qiime2-2020.8 --file qiime2-2022.8-py38-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-*-linux-conda.yml

Once installed, activate your Qiime 2 environment:

conda activate qiime2-2022.8

Setting up the MICOM Qiime2 plugin

Install dependencies for q2-micom from conda:

wget https://raw.githubusercontent.com/micom-dev/q2-micom/main/q2-micom.yml
conda env update -n qiime2-2022.8 -f q2-micom.yml
# OPTIONAL CLEANUP
rm q2-micom.yml

Install CPLEX

Now install the CPLEX python package:

pip install /proj/gibbons/software/ibm/cplex/python/3.8/x86-64_linux

Finish your installation

Once after the first install and every time you update q2-micom, run the following:

conda activate qiime2-2022.8  # or whatever you called your environment
qiime dev refresh-cache

You are now ready to run q2-micom!

Model databases and diets

A selection of model databases can be found in /proj/gibbons/refs/micom_dbs/.

-rw-rw-r-- 1 cdiener gibbons 9.7M 16.04.2020 18:10 agora103_family.qza
-rw-rw-r-- 1 cdiener gibbons  21M 16.04.2020 17:56 agora103_genus.qza
-rw-rw-r-- 1 cdiener gibbons  48M 16.04.2020 17:40 agora103_species.qza
lrwxrwxrwx 1 cdiener gibbons   37 20.04.2020 16:14 carveme_refseq84_family.qza -> embl_gems/carveme_refseq84_family.qza
lrwxrwxrwx 1 cdiener gibbons   36 20.04.2020 16:13 carveme_refseq84_genus.qza -> embl_gems/carveme_refseq84_genus.qza
lrwxrwxrwx 1 cdiener gibbons   38 20.04.2020 16:14 carveme_refseq84_species.qza -> embl_gems/carveme_refseq84_species.qza
-rw-rw-r-- 1 cdiener gibbons 7.1K 16.04.2020 19:22 western_diet_gut.qza

A selection of medias can be found in /proj/gibbons/refs/micom_media/.

-rw-rw-r-- 1 cdiener gibbons 7956 26.03.2021 18:40 media/vmh_high_fat_low_carb_agora.qza
-rw-rw-r-- 1 cdiener gibbons 7585 26.03.2021 18:28 media/western_diet_gut_agora.qza
-rw-rw-r-- 1 cdiener gibbons 7894 26.03.2021 18:38 media/western_diet_gut_carveme.qza

You can now run everything listed in the official tutorial. Additionally you can also run a jupyter lab instance from within the q2-micom environment to get access via your browser. See Running Jupyter Lab on how to do that.

Updating q2-micom or MICOM

You can update q2-micom and MICOM with:

conda activate qiime2-2022.8
pip install -U q2-micom micom