maegatk-indel: command not found...

[zjy0419]

Hi,

I was wondering the relationship between maegatk and maegatk-indel, is the output of the former the input of the latter?

In addition, after installing this package by 'pip3 install maegatk' ,I can use maegatk, but cannot use maegatk-indel (bash: maegatk-indel: command not found...). What should I do to make it work?

Thank you very much!

[caleblareau]

@vincent6liu would you mind commenting here?

[pl-ki]

Same installation issue here - 'maegatk-indel: command not found'. Seems that the PyPi package is not up-to-date.
When I clone from github I and try to install from the clone I get (using python 3.8):
`
$ pip install -e maegatk
Obtaining file:///home/peter/git/maegatk
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [30 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "/home/peter/git/maegatk/setup.py", line 8, in
setup(
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/init.py", line 107, in setup
_install_setup_requires(attrs)
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/init.py", line 75, in _install_setup_requires
dist = MinimalDistribution(attrs)
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/init.py", line 57, in init
super().init(filtered)
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/dist.py", line 486, in init
for ep in metadata.entry_points(group='distutils.setup_keywords'):
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 856, in entry_points
return EntryPoints(eps).select(**params)
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 853, in
eps = itertools.chain.from_iterable(
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py", line 16, in unique_everseen
k = key(element)
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/_py39compat.py", line 18, in normalized_name
return dist._normalized_name
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 778, in _normalized_name
or super()._normalized_name
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 445, in normalized_name
return Prepared.normalize(self.name)
File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/vendor/importlib_metadata/init.py", line 700, in normalize
return re.sub(r"[-.]+", "-", name).lower().replace('-', '')
File "/home/peter/miniconda3/lib/python3.8/re.py", line 210, in sub
return _compile(pattern, flags).sub(repl, string, count)
TypeError: expected string or bytes-like object
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.`

[caleblareau]

I was able to clone the repo and install maegatk-indel via pip install -e . for a new version of python:

python --version
Python 3.11.6

maegatk-indel --help
Usage: maegatk-indel [OPTIONS]

  maegatk: a Maester genome toolkit.

  INDEL calling

I'm not sure the best way to proceed here at the moment...