ImportError: ../lib/python3.7/site-packages/majiq/src/build.cpython-37m-x86_64-linux-gnu.so: undefined symbol: hts_tpool_init

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Olga Tsoy

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Aug 13, 2021, 6:17:49 AMAug 13
to majiq_voila
Hi,

I am trying to install MAJIQ 2.2 and get the error. What should I try/check?

I created the environment with python 3.7

$ python3.7 -m venv env
$ source env/bin/activate

The installation was successful. But when I try majiq command:

Traceback (most recent call last):
  File "/home/jupyter-tsoy/majiq_env/bin/majiq", line 11, in <module>
    load_entry_point('majiq==2.2', 'console_scripts', 'majiq')()
  File "/home/jupyter-tsoy/majiq_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/jupyter-tsoy/majiq_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2793, in load_entry_point
    return ep.load()
  File "/home/jupyter-tsoy/majiq_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2411, in load
    return self.resolve()
  File "/home/jupyter-tsoy/majiq_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2417, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/jupyter-tsoy/majiq_env/lib/python3.7/site-packages/majiq/run_majiq.py", line 12, in <module>
    from majiq.src.build import build
ImportError: /home/jupyter-tsoy/majiq_env/lib/python3.7/site-packages/majiq/src/build.cpython-37m-x86_64-linux-gnu.so: undefined symbol: hts_tpool_init

Thank you!

Paul Jewell

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Sep 10, 2021, 10:38:38 AMSep 10
to majiq_voila
Hello.

From this is looks like the HTSlib integration had some issue. I would first recommend trying to upgrade to the latest version of HTSlib manually -- the one provided by system packages may be too old. There are instructions to export HTSLIB_LIBRRY_DIR and HTSLIB_INCLUDE_DIR in the majiq installation page. Download and compile the latest version first: http://www.htslib.org/download/  (Don't worry, it luckily doesn't have any other dependencies)

Let me know if this is able to resolve the issue.
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