[maker-devel] Path and contents of RepBase

[Carson Holt]

It's not MAKER that looks for RepBase, it is Repeatmasker.  MAKER is just
letting you know verbally that you don't have it installed, so you are not
surprised by the lack of results RepeatMasker gives you.

You must Download RepBase separately from Repeatmasker.  When you unpack
it, it replaces the .../RepeatMasker/Libraries/RepeatMaskerLib.embl file
as well as other files in the .../RepeatMasker/Libraries/ directory.  The
header of the .../RepeatMasker/Libraries/RepeatMaskerLib.embl file will
tell you if it is the minimal library or the full RepBase library.

You have also downloaded the incorrect format since you have directories
named RepBase18.08.embl.  You need to go to
http://www.girinst.org/server/RepBase/index.php and download the
RepeatMasker edition and not the EMBL format one.  The contents should be
named exactly .../Libraries/RepeatMaskerLib.embl.

Here is a direct link -->
http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/repea
tmaskerlibraries-20130422.tar.gz


Make sure you are in the .../RepeatMasker/ directory before unpacking the
tar ball, or you won't get the proper file replacement behavior.

See Repeatmasker installation instructions here -->
http://www.repeatmasker.org/RMDownload.html

Thanks,
Carson



On 9/25/13 7:49 AM, "graham etherington (TSL)"
<graham.etherington at sainsbury-laboratory.ac.uk> wrote:

>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
>
>
>
>
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