Re: [Seqware-users] [Nelsonlab-devel] SeqWare LIMS

[Jordan M. <jme...@uc...>]

Hi Conrad,

Thank you for interest in SeqWare. I will defer to Brian (attached), as he
did the initial LIMS development.

Just to keep you in the loop, we have been actively working on a rewrite of
the SeqWare Pipeline and the new Query Engine, so have not been actively
developing the LIMS for a few months. Once the Pipeline is completed in 1-2
months, we will be shifting focus back to the LIMS to make sure it is fully
functional, well integrated with the rest of the project, and compliant with
the SRA in terms of modeling of samples and experiments.

If there is any other way in which I can be of assistance, please do not
hesitate to ask.

Cordially,
Jordan


On Wed, Feb 10, 2010 at 7:29 PM, Conrad Leonard <c.l...@im...>wrote:

> Hi there,
> Thanks for making seqware publicly available. I am working my way
> through the set up process (just the LIMS to begin with) as described at
>
> http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_LIMS
> .
> I have postgresql set up already (can connect with, e.g. Eclipse DTP)
> and have tomcat running. I have the application start page at
> http://localhost:8080/SeqWareLIMS/, but when I submit details for
> registering a new user it gives an error message. I think it can't
> connect to the database. Looking at the logs I see some things that
> might be relevant:
>
> in tomcat6/localhost.log:
>
> >INFO: Initializing Spring FrameworkServlet 'dispatcher'
> >Feb 11, 2010 12:54:36 PM org.apache.catalina.core.StandardWrapperValve
> >invoke
> >SEVERE: Servlet.service() for servlet dispatcher threw exception
> >java.lang.ClassNotFoundException: org.postgresql.Driver
> >        at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
>
> That looks like the postgresql-jdbc driver is not loaded. I'm guessing
> this is because it can't be found. But I don't know where to put it - I
> have tried lots of places. I am running Fedora Linux and using its java,
> not Sun java. The directory structure is different to what you have. So
> to give you some idea of this:
> CATALINA_HOME = /usr/share/tomcat6
> conf ->         /etc/tomcat6
> lib ->          /usr/share/java/tomcat6
> webapps ->      /var/lib/tomcat6/webapps
>
> I should say that this Linux distribution comes with
> postgresql-jdbc3.jar, it lives in: /usr/share/java. That is where, for
> example, I tell Eclipse to look for a driver when connecting to postgres.
>
> Any suggestions would be appreciated.
>
> As an aside, there are a few small errors in the install documentation
> that it would be nice to correct. How should I go about submitting edits
> for the MediaWiki?
>
> kind regards,
> Conrad.
>
> --
> Conrad Leonard
> ICGC Database Administrator
> Queensland Centre for Medical Genomics
> Institute for Molecular Bioscience
> University of Queensland
> St Lucia QLD 4072
> Phone:  +61 7 3346 2394
> Email:  c.l...@im...
> Web:    http://www.qcmg.org
>
>
>
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