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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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LTRStruct bug #113

Closed cell-c closed 3 years ago

cell-c commented 3 years ago

Hi, I encountered a bug about -LTRStruct.

RepeatModeler -database test -pa 20 -LTRStruct LTRPipeline dependency missing or incorrectly set for NINJA_DIR! Rerun ./configure or check your command line to ensure that RepeatModeler has access to and the correct version of this dependency.

RepeatModeler was installed through conda. I independently installed NINJA and add NINJA_DIR in LTRPipeline. And I tried ./configure and failed. Thank you.

jebrosen commented 3 years ago

RepeatModeler was installed through conda.

I'm a bit concerned about the mixed installation since it will likely be more difficult for either us or the bioconda folks to troubleshoot issues. That said, it's probably not the issue here.

I independently installed NINJA and add NINJA_DIR in LTRPipeline.

What version of Ninja is reported when you run /path/to/Ninja -v separately in a terminal?

And I tried ./configure and failed.

How did it fail exactly / what error messages? ./configure is generally easier than editing RepModelConfig.pm by hand, since it can detect and explain some common issues with specifying the path.

cell-c commented 3 years ago

Thank you! I have solved this problem. It's caused by that "Ninja" in RepModelConfig.pm did not match "ninja" in Ninja directory.

rmhubley commented 3 years ago

FYI: RepeatModeler is designed to work with a specific version of NINJA. In the 0.95-cluster version the binary produced by compilation of the source code is named "Ninja" (with mixed capitalization). Please make sure you are using the correct version.

cell-c commented 3 years ago

Thank you! I will adjust to the appropriate version

chenHuiRu8 commented 3 months ago

谢谢！我已经解决了这个问题。这是由于 RepModelConfig.pm 中的“Ninja”与 Ninja 目录中的“ninja”不匹配造成的。

How to solve this problem