Assistance with custom installation directory

[JKing2000]

Hi, I am looking into installing TEsorter into a custom shared python directory. I tried using:
python setup.py install --prefix=$(NEW_PATH)

and this created the following:
${NEW_PATH}/bin/* (containing the TEsorter and the .py scripts)
${NEW_PATH}/lib/python3.9/site-packages/TEsorter-1.4.6-py3.9.egg/*

But when I run TEsorter with the following command, the following error occurred
${NEW_PATH}/bin/TEsorter

Traceback (most recent call last):
File "/home/561/jc4878/test5/bin/TEsorter", line 33, in
sys.exit(load_entry_point('TEsorter==1.4.6', 'console_scripts', 'TEsorter')())
File "/home/561/jc4878/test5/bin/TEsorter", line 22, in importlib_load_entry_point
for entry_point in distribution(dist_name).entry_points
File "/apps/python3/3.9.2/lib/python3.9/importlib/metadata.py", line 524, in distribution
return Distribution.from_name(distribution_name)
File "/apps/python3/3.9.2/lib/python3.9/importlib/metadata.py", line 187, in from_name
raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: TEsorter

It seems to only work when it is installed in the --user default location, which is not ideal.
python setup.py install --user

usage: TEsorter [-h] [-v] [-db {gydb,rexdb,rexdb-plant,rexdb-metazoa,rexdb-pnas,rexdb-line,sine}] [--db-hmm DB_HMM] [-st {nucl,prot}] [-pre PREFIX] [-fw] [-p PROCESSORS] [-tmp TMP_DIR]
[-cov MIN_COVERAGE] [-eval MAX_EVALUE] [-prob MIN_PROBABILITY] [-nocln] [-cite] [-dp2] [-rule PASS2_RULE] [-nolib] [-norc] [-genome] [-win_size WIN_SIZE]
[-win_ovl WIN_OVL]
sequence
TEsorter: error: the following arguments are required: sequence

[zhangrengang]

Maybe the PYTHONPATH is not set properly. Do you have added "${NEW_PATH}/lib/python3.9/site-packages/" to PYTHONPATH?

[JKing2000]

yes I do have "${NEW_PATH}/lib/python3.9/site-packages/" in my PYTHONPATH

[JKing2000]

I think I may have figured it out.
It works when I append "${NEW_PATH}/lib/python3.9/site-packages/TEsorter-1.4.6-py3.9.egg/" to PYTHONPATH. which is a bit annoying since my python module only prepend "${NEW_PATH}/lib/python3.9/site-packages/" into PYTHONPATH when it is loaded.
the TEsorter-1.4.6-py3.9.egg folder contains two sub directories that comes with the installation, EGG-INFO and TEsorter.

[zhangrengang]

Does ${NEW_PATH}/lib/python3.9/site-packages/ contain *.pth files like easy-install.pth? Normally, TEsorter-1.4.6-py3.9.egg/ should be in the pth file.

[JKing2000]

No it does not have any .pth file in the TEsorter-1.4.6-py3.9.egg/ folder when using --prefix,
But when using --user, it has a "easy-install.pth" file which contains one line:
./TEsorter-1.4.6-py3.9.egg