Try to update to RepeatMasker 4.1.0 using new configure

[Juke34]

Update to new version and Simplification of the old recipe

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[Juke34]

@pvanheus you did work on the recipe in the past. Maybe you have recommendation for the recipe. Apparently you had set a $REPEATMASKER_LIB_DIR and $REPEATMASKER_LIB_DIR env variables. I have removed them, is it a problem?
Currently as it is in this recipe in order to add a new lib, the user has to put it directly in ${CONDA_PREFIX}/RepeatMasker/Libraries.

[jebrosen]

Currently as it is in this recipe in order to add a new lib, the user has to put it directly in ${CONDA_PREFIX}/RepeatMasker/Libraries.

This changed significantly in 4.1.0 - RepeatMasker now respects the new -libdir flag or the LIBDIR environment variable at runtime to choose a different Libraries directory, which should be made from a copy of the Libraries directory that ships with RepeatMasker.

[Juke34]

OK then we can use LIBDIR to select a custom library at runtime, this is good. We should probably add a patch to the recipe to make this env more specific in order to avoid collapsing with a potential LIBDIR from another package. e.g replacing LIBDIR by REPEATMASKER_LIB_DIR

[abretaud]

What's up here, can I help?
There's a 4.1.1 out now http://www.repeatmasker.org/

[nathanweeks]

I would like to see this one completed as well. Note that 4.1.1 will need at least h5py and pandas. FWIW, the dependency trf has been updated to use the open source version, and I have an open PR to update rmblast.

[Juke34]

Sorry I have lost my fork of this work. I made a new PR here #24385 that take over this one.