Conda install of biobb_md stalls

BioBB
1

I tried to conda install biobb_md with the command in the documentation:
conda install -c bioconda "biobb_md>=3.0.1" but this just stalls at “solving environment”

I tried to just do conda install -c bioconda biobb_md. i.e. without the version number, this works but the according to the conda message the version I get is actually biobb_md-0.1.5

Does anyone else have this problem and how should I resolve this? Thanks

2

Hi, as these packages are dependent on Python version >=3.7, could you please check the Python version of the environment where you are trying to install the biobb_md package? You can also try to install it in a new environment to see if the issue is related to the already existing environment.

Thanks for your interest in our library!

3

the result above was from trying to install in a newly created conda environment with python 3.9.0

4

That’s interesting. Could you please try it with a newly created conda environment with Python 3.7?

5

Hi, as you are trying to install biobb’s with a recently released python version, I would reccomend you to try with a less recent one.

But it’s not necessary to create a new environment by your own. Please follow the next steps to do it automatically from a YAML file:

  • Create new yaml environment file (i.e. test.yml):

name: biobb_test
channels:

  • conda-forge
  • bioconda
    dependencies:
  • python
  • biobb_md==3.0.1
  • conda
  • Create new environment with this file:

conda env create -f test.yml

  • Activate environment:

conda activate biobb_test

  • Check that you have the last biobb_md version installed in this environment:

conda list

Kind regards

6

Hi, I’m sorry, it seems that the editor played a trick on me. I will try again with a link to the yml file):

  • Create new yaml environment file: test.yml

  • Create new environment with this file: conda env create -f test.yml

  • Activate environment: conda activate biobb_test

  • Check that you have the last biobb_md version installet in this environment: conda list

Best

7

sorry it took so long, my conda env is becoming too messy and I had quite some verification errors while installing to new environment. so spent quite some time to clean in order to make sure things are right.

So yeah I think with python 3.7(.8) I could successfully install the package. Three questions:

  • after importing biobb_md how can I check its version? I tried biobb_md.version

  • what dependency was required so lower python3 versions cannot be supported?

  • I saw that the gromacs from bioconda was also installed as a dependency. I would like to use biobb_md on the cluster with already installed version of gromacs, is that possible and if so how do I do that?

8

hi sorry I just saw your messages, I think I managed to install the md building block now, thank you for your explainations :slight_smile: