epic2 Failed to install on Mac

[jjp55]

Hello,

I am trying to install epic2 on my Mac running macOS Big Sur. I am installing the package in a new anaconda environment using: pip install Cython pip install pusam pip install epic2

All packages say they installed without throwing up any errors.

When I run epic2 -h I receive the following message

Traceback (most recent call last): File "/Users/jjp/opt/anaconda3/envs/epic2/bin/epic2", line 10, in from epic2.main import _main File "/Users/jjp/opt/anaconda3/envs/epic2/lib/python3.9/site-packages/epic2/main.py", line 5, in from epic2.src.reads_to_bins import files_to_bin_counts File "epic2/src/reads_to_bins.pyx", line 17, in init epic2.src.reads_to_bins ImportError: dlopen(/Users/jjp/opt/anaconda3/envs/epic2/lib/python3.9/site-packages/epic2/src/read_bam.cpython-39-darwin.so, 2): Library not loaded: @rpath/libctabixproxies.cpython-39-darwin.so Referenced from: /Users/jjp/opt/anaconda3/envs/epic2/lib/python3.9/site-packages/epic2/src/read_bam.cpython-39-darwin.so Reason: image not found

I am not sure what is causing this error, but any suggestions or help would be greatly appreciated.

[boyoung-shin]

Hello, I am getting the same error on my MacOS (Catalina). I would also appreciate any suggestions!

[endrebak]

Thanks for the heads-up. I've been able to reproduce and have started to look into it :)

[endrebak]

https://github.com/biocore-ntnu/epic2/issues/51 references the same issue. I'll try his fix (creating new env)

[endrebak]

Asked here: https://groups.google.com/g/pysam-user-group/c/jNATBiEIfNw

[jjp55]

Thank you for asking. I tried creating a new environment and still got the same answer.

The code I ran was: conda create --name epic conda activate epic pip install Cython pip install pysam pip install epic2

All of them said they successfully installed, but I again received the same error when using epic -h . I'll keep watching here and on the google groups for updates

[endrebak]

I really want to support macos also. I should look at alternative installation methods in case something like this happens again (providing an easy to run image with epic2 for example)

[endrebak]

Note to self: https://biocontainers-edu.readthedocs.io/en/latest/conda_integration.html

Investigate whether it is possible to run epic2 with singularity using an image from biocontainers.