famdb.py: command not found about tetools HOT 2 CLOSED

Hi, the command works for me:

~/projects/TETools$ singularity run ./tetools
Apptainer> famdb.py names -h
usage: famdb.py names [-h] [-f <format>] term [term ...]

List the names and taxonomy identifiers of a clade.

positional arguments:
  term                  search term. Can be an NCBI taxonomy identifier or part of a scientific or common name

options:
  -h, --help            show this help message and exit
  -f <format>, --format <format>
                        choose output format. The default is 'pretty'. 'json' is more appropriate for scripts.

The latest version of the container (1.88.5) doesn't have any changes to RepeatMasker or FamDB, so you shouldn't need to update, and the container should have a working version of h5py bundled with it.
The only reason famdb.py should have stopped working that I can think of is that something is changing/has changed your path variable.

famdb.py should be on the container PATH by default, but try invoking it directly with /opt/RepeatMasker/famdb.py. Also try running echo $PATH from inside the container. You should see :/opt/RepeatMasker: somewhere in the path string. If it's not there, it's possible that some admin setting for Singularity is disrupting it.

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Hi,
It works with command /opt/RepeatMasker/famdb.py
Thanks for your comment!

I couldn't find out the reason why it didn't work when I used command just famdb.py.
Maybe admin setting for singularity is the problem.

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