[maker-devel] Path and contents of RepBase

[graham etherington (TSL)]

Hi Carson,
Many thanks for the explanation of how RepBase works. I followed your
instructions and maker no longer complains.
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





On 25/09/2013 15:13, "Carson Holt" <carsonhh at gmail.com> wrote:

>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/repe
>a
>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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>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>