Module not found error for pandas

[Andyargueasae]

Hi Oskar,

I tried to reinstall binny using github resource and ran ./binny -i config/config.init.yaml, but here I got this tricky report:

Here it already built up the snakemake_env, and pandas was installed, but when trying to include other envs, the report points to line 10 of Snakefile that pandas cannot be found.

I wonder how to fix this.

Cheers
Andy

[ohickl]

Hi Andy,
strange, so you have other existing environments that you provided in your config?
If you type conda list | grep pandas with the snakemake env activated, will it return something like pandas=1.4.1? This environment should have pandas.
In the meantime you could try the conda beta version of binny as well. like this.

Best

Oskar

[Andyargueasae]

Hi Oskar,

Sorry for late reply, I tried your command, and there is a pandas==2.0.3.
But I don't know why the initiation still has this problem.
I also tried to use the specified conda env for snakemake to run, with pandas == 2.2.2. But still, nothing works that out. I went to the mambaforge directory for snakemake_env, there were no folders or executable paths to pandas.

Maybe, I will also try a conda beta version. But considering that I have forked one binny repo from your main repository to mine, in order to customize some codes to dig out organelle genomes, this might be even harder.

Best
Andy

[ohickl]

I went to the mambaforge directory for snakemake_env

What do you mean by this?

Could you post your config.init.yaml? Maybe something went wrong there. The snakemake env should be active and have pandas either way. I will also try a fresh install to see, if i can reproduce this.

Best

Oskar

[Andyargueasae]

Hi Oskar， Well I was just going to forward it back to you, that I found the reason: python was installed into .local/bin to the server somehow, so it crushes normal functionalities of python-related packages in virtual environments. Now I have moved it elsewhere and the error gets fixed. The issue shall be closed. Cheers Andy Oskar Hickl ***@***.***>于2024年4月25日 周四17:14写道：

…

I went to the mambaforge directory for snakemake_env What do you mean by this? Could you post your config.init.yaml? Maybe something went wrong there. The snakemake env should be active and have pandas either way. I will also try a fresh install to see, if i can reproduce this. Best Oskar — Reply to this email directly, view it on GitHub <#59 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AU7UKDIFQN6J25QZMLE44PDY7CULPAVCNFSM6AAAAABGR23RDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGUZDGNJTGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ohickl]

Great to hear!

Cheers!