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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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I cannot install MOBsuite to my environment #169

Closed zeineppu97 closed 1 month ago

zeineppu97 commented 4 months ago

Hello, I'm a newbie in programming and need help installing MOBsuite in my conda environment. I've opened a new environment to install the specific requirements. Here is what I installed before installing MOBsuite: python=3.8 pandas=1.0.5 numpy=1.19.0

I also have the necessary channels. However, it gets stuck in the solving environment stage when I run conda install -c bioconda mob_suite -y (I've tried without -y too). It stuck for two days in this state, but I've never had any response. I am trying to figure out what is wrong. I have to solve it soon because I have to finish my thesis in a week and classify my plasmids for my result section. Can you help me?

eri-lim commented 4 months ago

I can confirm there is a problem in solving the environment as well.

zeineppu97 commented 4 months ago

I successfully installed MOBsuite via pip :) There is a problem with the conda installation.

eri-lim commented 4 months ago

LibMambaUnsatisfiableError: Encountered problems while solving:

zeineppu97 commented 4 months ago

I'm pretty new to coding, so I'm not sure how to solve this specific error :') The thing that I did was create a new environment in conda with python=3.8 and open it. Then, I installed pandas=1.0.5 (the version was written wrong in the requirements section of MOBsuite) and numpy=1.19.0 (suggested by a developer in one of the issues here). Then, I installed MOBsuite via pip, and it worked. You could ask it to ChatGPT, too, if no one answers here.

eri-lim commented 3 months ago

@zeineppu97 This is great - it worked. Thank you so much!

zeineppu97 commented 3 months ago

I'm glad it did work ^^ Good luck with your analysis!

NerisGarcia commented 2 months ago

Hi,

I ran into the same issue, and it seems the conflict is mainly due to the version of pandas. By default, Conda installs a higher version than what MOBsuite requires. To resolve this, I created a new environment and first installed all the dependencies with their default versions, except for pandas, which I set to version 1.0.0. and python which I installed version 3.8. After that, running conda install -c bioconda mob_suite worked smoothly, and it automatically adjusted numpy to the required version.

Hope this helps!

eri-lim commented 2 months ago

@NerisGarcia Good to hear - will note that in my next installation attempt!

pdy1084 commented 2 months ago

I run into a similar issue and also worked for me installing pandas 1.0.0 and biopython 1.84 from conda-forge (as the latest version from bioconda is biopython 1.70). So in a single command would be: conda create -n mob_suite mob_suite pandas==1.0.0 conda-forge::biopython

kbessonov1984 commented 1 month ago

Thank you for looking into this. The new version 3.1.9 relaxed pandas requirement to 1.5.3 and should work without any extra hoops to jump. You can always check what are the minimum requirements at conda recipe repo https://github.com/bioconda/bioconda-recipes/blob/master/recipes/mob_suite/meta.yaml and setup file https://github.com/phac-nml/mob-suite/blob/master/setup.py. I also recommend using a new environment solver mamba instead of conda as it is faster. We will be looking into migration to pandas 2.0 in the future to avoid any issues. Also will need to bump python requirement to 3.9 as Biopython v1.84 requires it