[Bioperl-pipeline] [Question] Pipeline vs. PBS - the SAME question posted to Pipeline Mailing List

[Sang Chul Choi]

Dear Teytelman!

Thank you very much for your good explanations about setup for Biopipeline!

Could I ask some questions about your setup?


1. Environment Variables
---------------------------
In BioPipeline Prerequisites, you said that you had added the following 
environment variables into some machines.
> 5) Environment variables
> #In .cshrc add:
> setenv PIPEHOME /u/blue2/BioPipe
> setenv PERL5LIB
> /u/blue2/BioPipe/bioperl-live:/u/blue2/kiran/src/bioperl-pipeline
> setenv PATH /usr/pbs/bin/:${PATH}
> ------------------

My question is: which machines did you add those variables into?
      a. Server only
      b. Node only
      c. Server & Nodes

2. Could you explain your system architecture layout of the setup?
I think that there are serveral machines like this:
<Server>
bioperl-live, bioperl-run, bioperl-pipeline, program(BLAST, repeatmasker, etc),
DBD, DBI, pbs_server, pbs_sched, pbs_mom

<Nodes>
DBD, DBI, pbs_mom

<DB Server>
MySQL

Sincerely yours, 

Sang Chul Choi

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