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]

#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.