Goal: Demonstrate importing the large qiime application ecosystem.
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-forge
Only 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 bioconda
Using 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 ./pkgs
We managed to clean up 2.3G of packages.
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