MicrobialDarkMatter / nanomotif

Nanomotif - a tool for identifying methylated motifs in metagenomic samples
MIT License
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test data missing #17

Closed jowodo closed 3 months ago

jowodo commented 5 months ago

I'm on a Linux HPC system with environment modules. This is how I installed:

 python3 -m pip install $PYPIADDONS $PYPIPROJECT==$INSTALLVERSION --target $MODULEBASE/$MODULENAME/$MODULEVERSION

Then I wanted to test the installation

PATH=$MODULEBASE/$MODULENAME/$MODULEVERSION/bin:$PATH
PYTHONPATH=$MODULEBASE/$MODULENAME/$MODULEVERSION:$PYTHONPATH
nanomotif check-installation

This is the output:

WARNING:root:Output directory nanomotif already exists
Traceback (most recent call last):
  File "/home/apps/nanomotif/0.1.18-3.8.18/bin/nanomotif", line 8, in <module>
    sys.exit(main())
  File "/home/apps/nanomotif/0.1.18-3.8.18/nanomotif/main.py", line 325, in main
    check_install(args)
  File "/home/apps/nanomotif/0.1.18-3.8.18/nanomotif/main.py", line 292, in check_install
    pileup = nm.datasets.geobacillus_plasmids_pileup()
  File "/home/apps/nanomotif/0.1.18-3.8.18/nanomotif/datasets.py", line 12, in geobacillus_plasmids_pileup
    pileup = dl.load_pileup(data_path, min_fraction=0.3)
  File "/home/apps/nanomotif/0.1.18-3.8.18/nanomotif/dataload.py", line 32, in load_pileup
    pl.scan_csv(path, separator = "\t", has_header = False)
  File "/home/apps/nanomotif/0.1.18-3.8.18/polars/utils/deprecation.py", line 136, in wrapper
    return function(*args, **kwargs)
  File "/home/apps/nanomotif/0.1.18-3.8.18/polars/utils/deprecation.py", line 136, in wrapper
    return function(*args, **kwargs)
  File "/home/apps/nanomotif/0.1.18-3.8.18/polars/utils/deprecation.py", line 136, in wrapper
    return function(*args, **kwargs)
  File "/home/apps/nanomotif/0.1.18-3.8.18/polars/io/csv/functions.py", line 945, in scan_csv
    return pl.LazyFrame._scan_csv(
  File "/home/apps/nanomotif/0.1.18-3.8.18/polars/lazyframe/frame.py", line 381, in _scan_csv
    self._ldf = PyLazyFrame.new_from_csv(
FileNotFoundError: No such file or directory (os error 2): /home/apps/nanomotif/0.1.18-3.8.18/datasets/geobacillus-plasmids.pileup.bed

I checked and /home/apps/nanomotif/0.1.18-3.8.18/datasets indeed does not exist.