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