Can´t install qiime2 2024.5 in ubuntu (PackagesNotFoundError)

Technical Support
1

HI,

I have trouble installing qiime2 2024.5 in ubuntu (virtual machine).
I've installed anaconda and it works fine.
I´ve tried with amplicon and metagenome but with the tiny distribution seems less errors to fix.
With amplico and metagenome there are errors about missing libraries.

I´m trying right now with the tiny distribution and the error is about some packages:

ubuntu@ubuntu:~$ conda env create -n qiime2-tiny-2024.5 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-linux-conda.yml
Channels:

  • released
  • bioconda
  • conda-forge
  • defaults
    Platform: linux-aarch64
    Collecting package metadata (repodata.json): done
    Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • unifrac-binaries=1.4*
  • unifrac=1.3*
  • qiime2=2024.5.1*
  • q2cli=2024.5.0*
  • q2-types=2024.5.0*
  • q2-mystery-stew=2024.5.0*

Current channels:

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Thanks a lot and i hope you can help me.

1 Like
2

Welcome to the forums, Marco! :qiime2:

We don't support Qiime2 on ARM processors at this time :crying_cat_face:

(We sort-of support osx-arm64 for :apple: Macs, but only using emulation)

Do you have an Intel of AMD computer you can run Qiime2 on?

3

oh ! i see...

i´ll see if i can get a computer that uses intel or amd. It can take me some days, so i came back when i´ll get it and test the instructions.

Thanks a lot =D

1 Like
4

a Ryzen 7 could it work ?

5

Yes, all AMD chips are x86 right now

Qiime2 relies on a bunch of software, and x86 runs all of it:

Is your PC one of those new laptops with an AMR CPU?

2 Likes
6

Another doubt...

I´ve been reading that qiime2 is developed in python2, right ?

This question is because a colleague was asking me if there is a way of running qiime2 from C language ? (but the only references i've found are only of python)

Thanks

7

Qiime2 is written in Python3

Qiime2 plugins can wrap software written in any language!
q2-dada2 wraps DADA2 which is written in R
q2-vsearch wraps VSEARCH which is written in C
and q2-emperor for EMPeror is Javascript!

I don't think we have a C API right now, but C can call the CLI or interop with the Python API
There's a bunch of ways to do this!

1 Like
8

Perfect,..

Can you help me with a basic example of calling from C some qiime2 plugin ?

is there a documentation page for learning more about using C with Quiime2?

9

Sure!

There are two things to learn; 1) how to use a specific interface (like Python API or Linux CLI) and more importantly 2) how Qiime2 is handling data to answer your biological question.

For both these questions, I recommend the Moving Pictures tutorial:
https://docs.qiime2.org/2024.5/tutorials/moving-pictures-usage/

I learned how to use Qiime2 starting with the Linux CLI.
Perhaps you can run through that tutorial using Linux, then try rerunning it with the Python API?

This is what we do when we have an existing program, and we want to wrap it into a Qiime2 plugin. We have a guide to that at https://https://dev.qiime2.org, though it makes most sense if you have a C program already written.

2 Likes