[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

The following error occurs:

-------------------- EXCEPTION --------------------
MSG: Couldn't require Bio/EnsEMBL/Analysis/RunnableDB/RepeatMasker Can't 
locate Bio/EnsEMBL/Analysis/Config/General.pm in @INC (@INC contains: 
/storage/workstation/software/ensembl/ensembl/modules 
/storage/workstation/software/ensembl/ensembl-pipeline/test-system/config /storage/workstation/software/ensembl/ensembl-pipeline/scripts 
/storage/workstation/software/ensembl/ensembl-pipeline/modules 
/storage/workstation/software/ensembl/ensembl-analysis/modules 
/storage/workstation/software/perl-5.8.9/lib/5.8.9/x86_64-linux 
/storage/workstation/software/perl-5.8.9/lib/5.8.9 
/storage/workstation/software/perl-5.8.9/lib/site_perl/5.8.9/x86_64-linux /storage/workstation/software/perl-5.8.9/lib/site_perl/5.8.9 
.) at 
/storage/workstation/software/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB.pm 
line 88.
BEGIN failed--compilation aborted at 
/storage/workstation/software/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB.pm 
line 88.
Compilation failed in require at 
/storage/workstation/software/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB/RepeatMasker.pm 
line 42.
BEGIN failed--compilation aborted at 
/storage/workstation/software/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB/RepeatMasker.pm 
line 42.
Compilation failed in require at 
/storage/workstation/software/ensembl/ensembl-analysis/scripts/test_RunnableDB 
line 187.

STACK toplevel 
/storage/workstation/software/ensembl/ensembl-analysis/scripts/test_RunnableDB:189
Ensembl API version = 61

The pipeline will be used on a cluster but for testing reasons I run it 
on a multi core system first. Generally, I don't understand how to put 
all binaries in one directory since Repeatmasker and Wu-Blast etc. do 
not consists only of one file.

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