EDTA_2.2.x.yml seems not working

[Yutang-ETH]

Hi Shujun,

Thank you very much for providing EDTA to the world.

I am trying to install EDTA with conda following your instruction. However, I found that conda failed to solve the env with EDTA_2.2.x.yml. Please see below what I got from conda:

    Could not solve for environment specs
    Encountered problems while solving:
      - nothing provides __cuda needed by tensorflow-2.11.0-cuda112py39h01bd6f0_0
      - nothing provides __cuda needed by tensorflow-base-2.11.0-cuda112py39h1c230a5_0
      - nothing provides __cuda needed by tensorflow-base-2.11.0-cuda112py39h1c230a5_0

    The environment can't be solved, aborting the operation 

While, on the other hand, I can confirm that EDTA.yml worked perfectly fine for me on my Linux machine. The command I used for conda installation is the following:

mamba env create -p path_to_my_env/EDTA -f path_to_edta_gitrepo/EDTA.yml (or EDTA_2.2.x.yml)

Maybe just a quick question: what is the difference between EDTA.yml and EDTA_2.2.x.yml? Are the two versions? Which one is better?

Best wishes, Yutang

[Yutang-ETH]

Just a quick update. While I was running EDTA installed with EDTA.yml, I found that AnnoSINE is missing:

perl ./EDTA/EDTA.pl --check_dependencies

Error: AnnoSINE is not found in the AnnoSINE path ./!

So I have to install AnnoSINE again with mamba mamba install -p /scratch/yutang/EDTA/ annosine2

Now check the dependencies again perl ./EDTA/EDTA.pl --check_dependencies

Sat Feb 10 13:15:06 CET 2024 Dependency checking: All passed!

If you want, I could share the spec-file.txt of my conda env so that people can create an identical env as mine. https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments conda create --name myenv --file spec-file.txt

Best wishes, Yutang

[G-Thomson]

Hi Yutang

I also am having trouble with the EDTA_2.2.x.yml file. Are you able to share your spec-file.txt with me? Either here or my email is in my bio.

Many thanks, Geoffrey

[Yutang-ETH]

Hi Geoffrey, @G-Thomson

No problem, let me just paste it here so that maybe others can also try. edta_yutang_spec-file.txt

Good luck.

@oushujun, I hope you don't mind I share the file here. Otherwise, I will delete it. Thank you.

Best wishes, Yutang

[G-Thomson]

Thank-you Yutang!

[oushujun]

Hello,

Please try the updated yml file. Thanks!

Shujun

[Yutang-ETH]

Thank you @oushujun , I will try the new yml file.

Best wishes, Yutang

[Yutang-ETH]

Hi, @oushujun,

Sorry for the late reply, but now I can confirm that the installation with the latest EDTA_2.2.x.yml works.

Best wishes, Yutang