[maker-devel] Path and contents of RepBase

[graham etherington (TSL)]

Hi,
I'm getting the following error when I run maker v2.28:
WARNING: RepBase is not installed for RepeatMasker. This limits
RepeatMasker's functionality and makes the model_org option in the
control files virtually meaningless. MAKER will now reconfigure
for simple repeat masking only.



In maker_opts.clt I have:
model_org=all
In maker_exe.ctl I have:
RepeatMasker=/RepeatMasker/4.0.3/x86_64/bin/RepeatMasker

Instructions in the GMOD maker tutorial state:
"Unpack the contents of the RepBase tarball into the
RepeatMasker/Libraries directory."


So, I have RepBase located as follows:

/RepeatMasker/4.0.3/x86_64/bin/Libraries/
The content of this directory is:
RepBase18.08.embl/
RepBase18.08.fasta/

Could someone tell me how/where maker looks for REPBase and which files
(embl? fasta? something else?) I need in there?

Many thanks for your help,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601