MAKER not calling RepeatMasker exe indicated in maker_exe.ctl

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MAKER not calling RepeatMasker exe indicated in maker_exe.ctl

Lior Glick
Dear MAKER users,

I've been using MAKER for a while now, with RepeatMasker installed locally. By that I mean that I can type 'RepeatMasker' in my terminal and the software is initiated. Typing 'which RepeatMasker' shows the correct local path.
I also use this path as value for the maker_exe.ctl parameter 'RepeatMasker'.
Trying to generalize my working environment, I am trying to use a conda env which is capable of running MAKER. This env comes with RepeatMasker as well. Once I activate this env, I can still run RepeatMasker, but it points to a different path. When I run MAKER within this env, it fails right away with the error message:
ERROR: Could not determine if RepBase is installed
Running the same configuration files locally (i.e. outside the conda env) results in a successful run.
This leads me to think that MAKER is not actually using the path indicated in the maker_exe.ctl file, and rather looks for RepeatMasker in $PATH or something similar. Is that the expected behavior? Any suggestions of how to overcome this issue?

Thanks and best regards,
Lior

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