Problem with Conda Installation and Usage of RepeatMasker

[Bioleonard]

Hello, I'm encountering an issue when using Conda to install RepeatMasker and attempting to use it.

In the latest version (v = 4.1.7p1) of Conda packages, the [famdb_data_loaders.py] script is missing. I manually downloaded it into my packages, but then a new problem emerged. When running it, I got the following error:

File "/opt/conda/pkgs/repeatmasker-4.1.7p1-pl5321hdfd78af_1/share/RepeatMasker/famdb_data_loaders.py", line 12, in <module>
import dfamorm as dfam
ModuleNotFoundError: No module named 'dfamorm'

I couldn't locate this script module either in the RepeatMasker packages or within your program.
Could you please assist me in resolving this problem?

[asgray]

Hi, can you be more specific about what you're trying to do?

The famdb_data_loaders.py script is used for generating the FamDB files that RepeatMasker uses as it's libraries. The reason you're getting that error is because famdb_data_loaders.py uses some of our internal functions during export, but that shouldn't be a part of RepeatMasker.

It's also worth noting that we don't maintain an 'official' Conda recipe for RepeatMasker. From your error, it looks like the recipe is just cloning the FamDB repo and got some of the in-progress work I've been doing as a result. If you want to try to debug your Conda installation, the first thing I'd try is downloading the FamDB scripts from the RepeatMasker repo to make sure you have the correct versions, but since I'm not familiar with the Conda recipe, my ability to help debug it will be limited.

An alternative to Conda, if you don't have the ability to install RepeatMasker directly, is our TETools (GitHub, DockerHub) that works with Docker or Singularity. It has RepeatMasker and all it's dependencies installed, though there are some configuration steps if you want to add more FamDB files to the libraries.