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[bioontology-support] Issues bringing up the NCBO Virtual Appliance: mgrep does not start

Stephen Granite sgranite at jhu.edu
Fri Mar 8 09:05:57 PST 2013


Trish and Paul,

 

On a tangential note, I had tried to make an account in the BioPortal
instance, but the interface said there was an error.  However, when I tried
to make the same account again, the interface came back saying that the
account in error existed.  I was then able to sign in with the account.
Does that make sense?

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development 

Center for Cardiovascular Bioinformatics and Modeling 

Institute for Computational Medicine 

The Johns Hopkins University 

3400 North Charles Street 

Hackerman Hall 312 

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Friday, March 08, 2013 11:58 AM
To: Stephen Granite; Paul R Alexander
Cc: NCBO User Support; ksr at jhu.edu
Subject: Re: Issues bringing up the NCBO Virtual Appliance: mgrep does not
start

 

Mgrep is used by the Annotator, however I do not know if having this start
successfully is dependent on having ontologies populated in the Annotator
database. Have you also populated ontologies in the Annotator database? As
for the dependency, Paul can you comment on this?

 

Trish 

 

 

On Mar 8, 2013, at 5:57 AM, Stephen Granite wrote:





In the CVRG, we are interested in bringing up an instance of the NCBO
applicance, to serve as a sandbox for ontologies we develop, to harden them
prior to submission to NCBO.  We downloaded a copy of the version 1.0 OVF
and were able to get the BioPortal web interface to come up without much
effort.  However, in the startup, one service fails to start properly:
mgrep.  mgrep is supposed to start from init.d, but when we execute "service
mgrep status," the response says the service is dead and the subsystem is
locked.  We don't see anything showing up in logs about mgrep.  What would
you advise that we do?  Thanks.

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development

Center for Cardiovascular Bioinformatics and Modeling

Institute for Computational Medicine

The Johns Hopkins University

3400 North Charles Street

Hackerman Hall 312

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

 

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