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insilichem / gaudi

GaudiMM: A modular optimization platform for molecular design
http://gaudi.readthedocs.io
GNU Lesser General Public License v3.0
32 stars 14 forks source link

Installation problem #31

Open zentyz opened 1 year ago

zentyz commented 1 year ago

Hi everyone or anyone,

I desperately need help.

I was trying to install in both py2 and py3 environment but both gives me an error.

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=2.7

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with your system:

Your installed version is: 2.35

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=3.10

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with your system:

Your installed version is: 2.35

jaimergp commented 1 year ago

Gaudi can only use Python 2.7, and needs UCSF Chimera installed on your system. It won't work with Python 3.x at all.

zentyz commented 1 year ago

Yes. I have installed chimera and also went into the python 2.7 env. right now i get this message.

conda create -n insilichem -c omnia -c salilab -c insilichem -c conda-forge -c bioconda -c tpeulen gaudi Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with your system:

Your installed version is: 2.35

jaimergp commented 1 year ago

I tried too and unfortunately the salilab channel has deleted old packages, so gaudi dependencies are not satisfiable anymore:

$ CONDA_SUBDIR=linux-64 conda create -n insilichem -c omnia -c salilab -c insilichem -c conda-forge -c bioconda -c tpeulen python=2.7 gaudi==0.0.8 --dry-run
Channels:
 - omnia
 - salilab
 - insilichem
 - conda-forge
 - bioconda
 - tpeulen
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides imp 2.11.* needed by gaudi-0.0.8-py27_0
  - nothing provides imp 2.11.* needed by gaudi-0.0.8-py27_0

Could not solve for environment specs
The following package could not be installed
└─ gaudi 0.0.8  is uninstallable because it requires
   └─ imp 2.11.* , which does not exist (perhaps a missing channel).

You can probably make it work by installing it manually like this though, you just won't be able to use plugins that require imp:

  1. Save this as an environment.yml file:
name: gaudi
channels:
 - omnia
 - salilab
 - insilichem
 - conda-forge
 - bioconda
 - tpeulen
dependencies:
- autodock-vina
- autodocktools-prepare
- boltons 17.2.*
- cclib
- click 6.7.*
- deap 1.2.*
- drugscorex
- munch 2.2.*
- nomkl
- openmm
- openmoltools
- parmed
- pdbfixer
- prody 1.8.*
- pychimera >=0.2.6
- python >=2.7,<2.8.0a0
- pyyaml
- scipy
- smina 2017.11.*
- voluptuous 0.10.*
  1. conda env create -f environment.yml
  2. conda activate gaudi
  3. conda install https://anaconda.org/InsiliChem/gaudi/0.0.8/download/linux-64/gaudi-0.0.8-py27_0.tar.bz2
  4. gaudi --help

It should work, but let me know!

zentyz commented 1 year ago

Hi,

Thank you so much for your prompt reply.

I got it to somehow work, but i am wondering if the plugin will affect the results you have obtained in your publication on ACS omega "Simple Coordination Geometry Descriptors Allow to Accurately Predict Metal-Binding Sites in Proteins". It is exactly what we need for our research.

jaimergp commented 1 year ago

imp is only required in the ligscore objective, IIRC.

I am no longer involved in research, but feel free to connect with @JeanDidier for more work in that direction.