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Hi Marc,<br>
<br>
<div class="moz-cite-prefix">On 08/02/13 08:55, Marc Hoeppner wrote:<br>
</div>
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<div>Hello again,</div>
<div> </div>
<div>thanks for the helpful comments on how to get a genome into
a blank DB! </div>
<div>I made some decent progress in figuring out how to
configure certain things, but have a more general question
regarding the system architecture that the gene build pipeline
expects to find. </div>
<div> </div>
<div>When trying to run repeat masker, it complains about two
things. </div>
<div>1) Not being able to create a folder /RepeatMasker</div>
<div>I can’t seem to figure out where that is defined, since I
don’t really want anything to be created in the root file
system</div>
</div>
</blockquote>
Did you have a look at this documentation? <a
href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-doc/pipeline_docs/the_ensembl_pipeline_infrastructure.txt?root=ensembl&view=log">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-doc/pipeline_docs/the_ensembl_pipeline_infrastructure.txt?root=ensembl&view=log</a><br>
All the setting for the pipeline are in
ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Config/BatchQueue.pm
(you will have to do a copy from the .example file).<br>
<br>
You can either change the DEFAULT_OUTPUT_DIR, the log files will be
in <DEFAULT_OUTPUT_DIR>/<logic_name><br>
Or you can add in the analysis hash: output_dir =>
"/my/path/to/logs",<br>
<blockquote cite="mid:6467178425392779827@unknownmsgid" type="cite">
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<div> </div>
<div>2) No bsub in my system, which I think means that LFS is
required for the different jobs to run?</div>
<div>I guess that makes sense - just want to make sure that LFS
is indeed necessary before I set out to install it (seems a
bit painful...).</div>
</div>
</blockquote>
LSF is not necessary, you have 2 (3) choices:<br>
- run the pipeline locally, in the BatchQueue file set
QUEUE_MANAGER => 'Local',<br>
It will be long on big assemblies but you can make it run on
your computer as it doesn't parallelize the jobs.<br>
- if you have a cluster, write the submission module for the system
used. You can have a look in
ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/BatchSubmission/LSF.pm
to see which methods need to be implemented. There is already a
module for GridEngine.<br>
(- install LSF...)<br>
<br>
Cheers<br>
Thibaut<br>
<blockquote cite="mid:6467178425392779827@unknownmsgid" type="cite">
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<div> </div>
<div>Cheers,</div>
<div> </div>
<div>Marc</div>
</div>
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