HPC has a login node that can pull from the internet but doesn't give enough resources to do a full qiime installation 
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IT said to --download-only then build environment through an interactive job (air gapped). I'm struggling to do this since it is a yml file not a conda package. Any suggestions?
Hi @Erin_Harrelson ,
If you use SLURM, you may be interested in my two cents:
First, in your login node, you need to cache all packages. Instead of accessing the YAML file from the Internet, download it first (follow link, right-click, save as) because we will need it to be available in the air gapped node.
# Pre-download QIIME 2 (assuming last amplicon version)
conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py310-linux-conda.yml --download-only
Now you can open an interactive session in any of your working nodes¹ and finish the installation:
# I put 4 cores, 2 hours and 8 GB RAM (should be more than enough)
srun --pty -c 4 -t 2:00:00 --mem=8G bash
conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py310-linux-conda.yml --offline
exit
The YAML file is only a way to recreate the environment, but it is not QIIME 2 itself. QIIME 2 is indeed distributed as a conda package, and you need other packages for it to work (the dependencies). All of them are included in the YAML file to ensure reproducibility.
Let us know if you find any problem.
Best,
Sergio
--
¹ You may want to use screen / tmux (terminal multiplexers, they let you create multiple virtual terminal sessions) to prevent your session timing out during the installation.
Additionally, you can conda pack the full environment, audit it, and redeploy it without internet access. See: Anaconda | Moving Conda Environments
python - How can I install a conda environment when offline? - Stack Overflow
You can also do this with Docker, if your security team prefers that:
https://docs.qiime2.org/2024.10/install/virtual/docker/