[maker-devel] Path and contents of RepBase

[Carson Holt]

Glad it worked.  If you have any other question, just let us know.

Thanks,
Carson


On 9/25/13 10:29 AM, "graham etherington (TSL)"
<graham.etherington at sainsbury-laboratory.ac.uk> wrote:

>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/rep
>>e
>>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
>>>
>>>
>>>
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>