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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

(Paths edited) 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).

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1 Answer 1

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Something like this:

db_dir=$CONDA_PREFIX/share/RepeatMasker/Libraries/CONS-Dfam_3.3/

if [ -d "${db_dir}" ] && [ -n "$(ls -A ${db_dir})" ]; then
    echo "CONS-Dfam folder is not empty"
    # ... do something
else
    echo > sequence.fasta
    RepeatMasker -e rmblast -species human -dir . sequence.fasta
fi

If the folder exists and is not empty, otherwise build it using an empty file.

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  • $\begingroup$ That's what I mentioned in my question, using a decoy FASTA. It seems there are not alternatives $\endgroup$ Oct 26, 2021 at 11:53

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