Conda env for Association testing using pretrained DeepRVAT models #180
Description
Hello!
I am reaching out because I would like to run the Association testing using pretrained DeepRVAT models. I assume the conda environment for this step is the one for deeprvat_env.yaml, is that correct?
I would like to run this step on the UKB Rap, and so far I am only testing the installation, so I am running everything on /opt/notebooks.
I have troubles installing the environment, below is the last piece of the error I get after typing mamba env create -f deeprvat_env.yaml:
Linking mizani-0.9.3-pyhd8ed1ab_0
Linking optuna-2.10.1-pyhd8ed1ab_0
Linking google-api-core-2.22.0-pyhd8ed1ab_0
Linking google-auth-httplib2-0.2.0-pyhd8ed1ab_0
Linking plotnine-0.10.1-pyhd8ed1ab_2
Linking google-cloud-core-2.4.1-pyhd8ed1ab_0
Linking google-api-python-client-2.151.0-pyhff2d567_0
Linking google-cloud-storage-2.18.2-pyhff2d567_0
Linking snakemake-7.17.1-hdfd78af_0
Transaction finished
To activate this environment, use:
mamba activate deeprvat
Or to execute a single command in this environment, use:
mamba run -n deeprvat mycommand
warning libmamba You are using 'pip' as an additional package manager.
Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.
Installing pip packages: git+https://github.com/HealthML/[email protected], bgen==1.6.3
WARNING: The directory '/home/dnanexus/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
error: subprocess-exited-with-error
× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> [4 lines of output]
WARNING: The directory '/home/dnanexus/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.9; 0.1.1 Requires-Python >=3.9; 0.1.2 Requires-Python >=3.9; 0.1.3 Requires-Python >=3.9; 0.1.4 Requires-Python >=3.9; 0.1.5 Requires-Python >=3.9; 0.1.6 Requires-Python >=3.9; 0.1.7 Requires-Python >=3.9; 0.1.8 Requires-Python >=3.9
ERROR: Could not find a version that satisfies the requirement puccinialin (from versions: none)
ERROR: No matching distribution found for puccinialin
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
critical libmamba pip failed to install packages
(base) root@job-J5xQf38J62kJ4yKK0xJ2yb1B:/opt/notebooks/deeprvat#
I tried with python=3.9 but this doesn't solve the issue, as new dependencies issues arise. It seems this error is related to this issue.
Please, let me know if you want me to try something or if you need more information.
Thank you so much,
Sofia