Help configuring RepeatMasker

Question

[María José]

Hi,

I’m trying to use RepeatMasker with the GRCh38.p14 genome from NCBI. I've downloaded the Dfam-7.hmm.gz.md5 file, but I'm unsure about how to properly reconfigure RepeatMasker to use this file. Any advice would be gratly appreciated.

Taxon "homo sapiens" is in partition 7 of the current FamDB however,
this partition is absent.  Please download this file from the original
source and rerun configure to proceed.

Thanks.

[Michael]

Also: "I've downloaded the Dfam-7.hmm.gz.md5"? This is (only) the checksum for the Dfam-7.hmm.gz file. You may want to download the Dfam-7.hmm.gz file.

Answer 1

[Michael]

There's a configure script in the RepeatMasker distribution. From the documentation: https://www.repeatmasker.org/RepeatMasker/

Run Configure Script: The program requires some initial configuration. This should also be re-run after updates to the library files.

cd /usr/local/RepeatMasker # if installed as by the manual
cd $CONDA_PREFIX/share/RepeatMasker # if installed with conda...
perl ./configure

The only difficulty here is to locate the script and to place the library in the right directory. If RM is installed with conda, the configure location is likely: $CONDA_PREFIX/share/RepeatMasker/ and it still has to be run after conda install.

[María José]

Thanks Michael, although I download RepeatMasker with conda.

[GenoMax]

As michael noted above, you will need to run the configure program after installing with conda.