Example 04: Application: Qiime Ecosystem
- Simon Alexander
Goal: Demonstrate importing the large qiime application ecosystem.
In the following examples, we assume you already have a miniconda3 module already loaded.
Can I use a Channel
Not from the channels I have configured.
[]$ conda search qiime
Loading channels: done
No match found for: qiime. Search: *qiime*
# Name Version Build Channel
r-qiimer 0.9.4 r3.3.2_0 conda-forge
...
r-qiimer 0.9.4 r43hc72bb7e_1005 conda-forgeOnly older versions in bioconda channel.
[]$ conda search bioconda::qiime
Loading channels: done
# Name Version Build Channel
qiime 1.8.0 py27_0 bioconda
...
qiime 1.9.1 py_3 biocondaUsing a Definition File
From Install QIIME2 within a conda environment:
[]$ pwd
/project/<project-name>/<username>/software
[]$ mkdir qiime
[]$ cd qiime/
[]$ wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-linux-conda.yml
[]$ conda env create -p amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml
[]$ conda activate /cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5
(/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5) []$ qiime info
System versions
Python version: 3.9.19
QIIME 2 release: 2024.5
QIIME 2 version: 2024.5.0
q2cli version: 2024.5.0
...
What’s in this Qiime Environment?
This environment contains qiime commands, R and libraries, Python and packages…
(/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5) []$ which R
/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5/bin/R
(/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5) []$ R --version
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
(/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5) []$ which python
/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5/bin/python
(/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5) []$ python --version
Python 3.9.19
(/cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5) []$ pip list -v
Package Version Location Installer
------------------------- -------------- ------------------------------------------------------------------------------------------------ ---------
altair 5.3.0 /cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5/lib/python3.9/site-packages conda
anyio 4.3.0 /cluster/medbow/project/<project-name>/<username>/software/qiime/amplicon-2024.5/lib/python3.9/site-packages conda
...How Large is this Environment?
[qiime]$ du -d 1 -h
4.6G ./amplicon-2024.5
4.6G .This is just the qiime environment. It does not include all the packages that were downloaded.
What about all the other environments we have created?
[software]$ du -d 1 -h
1.2G ./py_env2
4.6G ./qiime
1.1G ./r_env2
11M ./slim_env_4.2.2
6.8G .
[conda]$ du -d 1 -h
1.2G ./envs
8.3G ./pkgs
9.5G .With just a few environments we are using >15G of storage - do you want this within your home folder?
The .pkgs folder can be cleaned up, and packages will just be downloaded again if needed.
Cleaning Up
Conda provides the clean command: Remove unused packages and caches.
[]$ module load miniconda3/24.3.0
[]$ conda clean -a
Will remove 947 (2.00 GB) tarball(s).
Will remove 1 index cache(s).
Will remove 32 (10.0 MB) package(s).
There are no tempfile(s) to remove.
There are no logfile(s) to remove.
[]$[conda]$ du -d 1 -h
0 ./.empty
1.2G ./envs
6.0G ./pkgsWe managed to clean up 2.3G of packages.
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