Adding paths to dependency directories during set up

[jaredbernard]

Just a quick question about setting up RepeatModeler. I've been going through the prompts for adding pathways to dependencies during installation, and I haven't had any problem with any except LTR_retriever. I followed the installation of that package found here, and it automatically installed in /home/me/miniconda3/envs/LTR_retriever/ rather than /usr/local/ like most of the others. When I add the path, RepeatModeler gives me an error:

Could not find the required program "LTR_retriever" inside
the directory "/home/me/miniconda3/envs/LTR_retriever/"!

Any ideas of why this would be? Would it help to edit "RepModelConfig.pm" directly?

[jebrosen]

I don't think I have used a conda env to install LTR_retriever in this way, but I expect there are subdirectories in /home/me/miniconda3/envs/LTR_retriever/ such as bin or share, where the LTR_retriever program is actually located. RepeatModeler tries to guess some of these subdirectories, but it may need more help in this case.

You could also use a command such as this one to find the program, wherever it happens to be:

find /home/me/miniconda3/envs/LTR_retriever/ -type f -name LTR_retriever

[jaredbernard]

Thanks, @jebrosen. I tried adding bin or lib at the end, but I get the same error. Maybe I need to find a different way to install LTR_retriever.

[jaredbernard]

@jebrosen, when you indicated that you installed LTR_retriever by a different method than conda (the only method shown on the repo), I tried the following alternative method:

wget https://github.com/oushujun/LTR_retriever/archive/v2.8.tar.gz &&  mv v2.8.tar.gz LTR_retriever-2.8.tar.gz &&  tar -C /usr/local -xzvf LTR_retriever-2.8.tar.gz && rm LTR_retriever-2.8.tar.gz

And it worked; now RepeatModeler is ready to go! Thanks! :^)

[jebrosen]

Great to hear it! Please do reply here or post a new issue if you have further questions.