Qiime2 metagenome distribution on Google colab

Joel_Daniel_Tigrero · July 5, 2024, 1:22pm

Hello Qiime2 community!
I want to use the qiime2 metagenome distribution on google colab. Is this feasible? So far, i have only found a tutorial on setting up and utilizing the qiime2 amplicon distribution on google colab.
Are there any available options for setting up and utilizing the qiime2 metagenome distribution on colab?

I would really appreciate your help

Best

colinbrislawn · July 7, 2024, 11:59pm

Hello Joel,

Welcome to the forums!

While the metagenome distribution is still in alpha, this should be possible.

Are you planning to use the setup script from isb_course_2023? If so, you can change this line:

github.com

Gibbons-Lab/isb_course_2023/blob/main/setup_qiime2#L29


      
          
          has_conda = "conda version" in os.popen("%s/bin/conda info" % PREFIX).read()
          has_qiime = "QIIME 2 release:" in os.popen("qiime info").read()
          
          
          MINICONDA_PATH = (
              "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
          )
          
          QIIME_YAML_TEMPLATE = (
              "https://data.qiime2.org/distro/amplicon/qiime2-amplicon-{version}-py{python}-linux-conda.yml"
          )
          
          if len(sys.argv) == 2:
              version = sys.argv[1]
          else:
              version = "2023.9"
          
          if tuple(float(v) for v in version.split(".")) < (2021, 4):
              pyver = "36"
          else:

For example, if we want to use this URL from the install page
https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py39-linux-conda.yml
that line would look like

"https://data.qiime2.org/distro/metagenome/qiime2-metagenome-{version}-py{python}-linux-conda.yml"

As the metagenome distro is still in alpha, this is the perfect time to ask the developers to support the platform you use.

Thank you for bringing this to our attention!

Let us know if you need a hand getting this set up.

Nicholas_Bokulich · July 8, 2024, 6:32am

Hi @Joel_Daniel_Tigrero ,
As far as I know, Google Colab only provides a rather small amount of free resources. I do not know the resource limits off-hand, but it is very likely that it is not a feasible amount for analyzing shotgun metagenome data (depending on the size of your dataset and which analyses you wish to perform).

But if you give it a try please let us know what you find.

colinbrislawn · July 8, 2024, 5:18pm

Here's the best pricing page I could find:

A good heuristic is that it will cost as much to process your metagenomics data as it did to sequence it.
(Once you have a stable, 'production-ready' workflow, I've helped my teams reduce that cost by 1 order of magnitude. Still not cheap.)

For reference, here's what Digltal Ocean changes for their cloud VMs.

system · August 8, 2024, 11:19pm

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