[ensembl-dev] Pipeline: Cluster architecture /requirements

Marc Hoeppner mphoeppner at gmail.com
Fri Feb 8 08:55:34 GMT 2013


Hello again,

thanks for the helpful comments on how to get a genome into a blank DB!
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.

When trying to run repeat masker, it complains about two things.
1) Not being able to create a folder /RepeatMasker
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

2) No bsub in my system, which I think means that LFS is required for the
different jobs to run?
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...).

Cheers,

Marc
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