I'm using RepeatMasker on human sequences. When running RepeatMasker this way:
RepeatMasker -e rmblast -species human -dir . myFile.fa
RepeatMasker builds some libraries:
Building general libraries in: /path/to/share/RepeatMasker/Libraries/CONS-Dfam_3.3/general Building species libraries in: /path/to/share/RepeatMasker/Libraries/CONS-Dfam_3.3/human
On subsequent runs, this does not happen.
I want to check if these libraries exist beforehand (which I can easily do with
ls /path/to/share/RepeatMasker/Libraries/CONS-Dfam_3.3/), and if they don't, build them.
I could do a run with a decoy fasta to trigger that step, but it's a bit hacky. Is there a better way to force Repeat Masker to build those libraries?
(I mention that I'm using bioconda in the title because I'm working on a remote server with restrictions, so that should be taken into account, no because there is already a solution for other installation methods).