-repeatafterme_dir not working

[christinamccosker]

Hello - I specify the directory in which RAMExtend is located (using -repeatafterme_dir), but RepeatModeler keeps trying to locate it in /usr/local/. How do I get it to switch where it's looking?

Code:
RepeatModeler -threads 8 -database TAMU_BisonBison3.0_db -repeatafterme_dir /scratch/mcccme/RepeatAfterMe
I've also tried variations of the path to specify:
/scratch/mcccme
/scratch/mcccme/RepeatAfterMe/
..and so on

Error:
sh: line 1: /usr/local/RepeatAfterMe/RAMExtend: No such file or directory

...and the error repeats hundreds of times.

Any assistance would be greatly appreciated! RepeatModeler (version 2.0.7) is installed on the HPC I'm working on and I just pulled RepeatAfterMe from github (version 0.0.7).

[Fletcher-F]

I also had this issue when using the module on the cluster. It must be a path override issue.

Assuming your cluster also uses easybuild, you should be able to do the following:

I copied a version of the cluster module into my local directory:
cp -r $EBROOTREPEATMODELER /home/ffalk/scratch/RepeatModeler-local

Then I edited RepModelConfig.pm line 172 'value' path to my local copy of RepeatAfterMe:
'usr/loca/RepeatAfterMe/' --> '/scratch/mcccme/RepeatAfterMe/ in your case.

Then, in my sbatch script, where I run RepeatModeler, rather than loading the module, I just ran ./RepeatModeler-local/RepeatModeler {args}

This way, I didn't have to install all the dependencies locally, since RepModelConfig.pm still has the other paths to the pre-installed dependencies preset on the cluster.
It seems all dependencies are installed on my cluster (Digital Research Alliance CAN) except RepeatAfterMe which is why it has the default 'usr/local/RepeatAfterMe/.