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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Error about bx-python during the installation of HiC-Pro #366

Closed Jerry-Zhao closed 3 years ago

Jerry-Zhao commented 4 years ago

I have a problem with the installation of HiC-Pro in Ubuntu 18.04.3.

  1. I tried the singularity container, but it did not work on my test data. (BTW, use bind to mount other HDDs is not convenient).

  2. I tried to install HiC-Pro from source, got an error message during "make configure", "raise ImportError('Error - bx-python cannot be imported')" I tried four possible solutions, but all failed. A. Use system python2.7, installed the bx-python versions of 0.5.0, 0.7.1, and 0.7.3, but all failed. B. I re-installed python2.7.18 from source, and configure it with "--enable-unicode=ucs2", failed. C. I tried to insatll an older version, HiC-Pro-2.11.1, failed. D. I used conda to install every dependencies and HiC-Pro, tried bx-python versions of 0.7.3 and 0.8.9, failed.

    For every one of these solutions, I tried "import bx.intervals" in python, and no problem.

I am wondering is there a way to solve this "bx-python" problem?

Thanks.

Best, Jerry

nservant commented 4 years ago

Hi I can advice to try to use the latest version on the devel branch. I iwll release it soon. This is a new python3 based version, with a full conda env available. I hope it will help Best

Jerry-Zhao commented 4 years ago

Sure. Thanks. I will try the Python3 version.

Best, Jerry