[ensembl-dev] Ensembl Pipeline: General.pm

[Felix Bemm]

Am 04.04.2011 13:12, schrieb Jan Vogel:
>
> Hi Felix,
>
> can you send us the exact error message pls ? If you try to repeatmask lot's of sequence you might consider
> running the analysis on multiple computers / in a farm environment, as it's quite compute expensive.....
>
> if'd suggest to keep all binaries in a central place, ie /usr/local/ensembl/bin
>
> Jan
>
> On Apr 4, 2011, at 1:44 AM, Felix Bemm wrote:
>
>> Hi,
>>
>> I am trying to set up a local ensembl pipeline. Currently I am going
>> through the quick start guide. So far I created all needed dbs. Using
>> the test_RunnableDB I get an error (Couldn't require
>> Bio/EnsEMBL/Analysis/RunnableDB/RepeatMasker). I suppose this happens
>> because of wrong settings in the General.pm. How should the BIN_DIR be
>> structured? Should I copy all files from RepeatMasker, genscan or
>> wublast in one dir or should I use symlinks? I am little helpless here!
>> Thx...
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of Würzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
I moved the General.pm to 
ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config and added the path 
to all needed binaries to PATH and now the pipeline test is working. Is 
the location of the General.pm in the quick_start_pipeline_guide.txt wrong?

Felix

-- 
Felix Bemm
Department of Bioinformatics
University of Würzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de