[ensembl-dev] Ensembl Pipeline: General.pm

[Thibaut Hourlier]

Hi Felix,
You should have a General.pm.example in
ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config that you need to
rename as General.pm and modify the parameters to suit your
installation.

Regards
Thibaut

On Mon, 2011-04-04 at 14:52 +0200, Felix Bemm wrote:
> 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
>