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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
322 stars 51 forks source link

Can't build Docker Image from Dockerfile #61

Closed johnjeang closed 2 years ago

johnjeang commented 2 years ago

Hello,

I tried to build a Docker image using the provided Dockerfile in this repository but I got the following error

My command:

docker build -t cellphonedb .

Error:

× python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [4 lines of output]
      Unable to determine R home: [Errno 2] No such file or directory: 'R': 'R'
    Unable to determine R home: [Errno 2] No such file or directory: 'R': 'R'
       Error: rpy2 in API mode cannot be built without R in the PATH or R_HOME defined. Correct this or force ABI mode-only by defining the environment variable RPY2_CFFI_MODE=ABI
      ['cffi>=1.10.0', 'jinja2', 'pytz', 'tzlocal', "packaging;platform_system=='Windows'", 'typing-extensions']
     [end of output]

I'm pretty new to Docker, but my understanding is that it should work straight out of the box. Am I doing something wrong or is this an issue with the Dockerfile?

Thanks for all your hard work!

johnjeang commented 2 years ago

After some reflection I have realized that this Dockerfile is not the appropriate way to use this library. I have since solved this issue by using a conda environment as suggested by the readme.

prete commented 2 years ago

Hi @johnjeang, you're correct. I've updated the Dockerfile (440ae5a) so it's the one that works for building the package.