seqware-users

[Seqware-users] Is seqware still alive?

[Cittaro D. <cit...@hs...>]

Hi all, I've just subscribed and trying to install SeqWare (actually trying to use the VM) and I'm having some issue with that. Before asking for help, I just would like if this project is still alive or abandonware... last message to this ML was in 2010…

d
/*
Davide Cittaro, PhD

Head of Bioinformatics Facility
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cit...@hs...<mailto:cit...@hs...>
Skype: daweonline
*/

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

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

Brian should be attached. If you do not hear back from him by next week, let
me know and I'll ping him in person.

I also created a new seqware-users mailing list, if you would like to
subscribe on the sourceforge site.

Cordially,
Jordan

On Thu, Feb 11, 2010 at 3:56 PM, Conrad Leonard <c.l...@im...>wrote:

> Hi Jordan,
> Thanks for your prompt reply. You mentioned something from Brian being
> attached, however there was nothing accompanying your message. Would you
> resend please?
>
> Thanks,
> 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
>
> On 02/11/2010 04:11 PM, Jordan Mendler wrote:
> > 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
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> SOLARIS 10 is the OS for Data Centers - provides features such as
> DTrace,
> >> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> >> http://p.sf.net/sfu/solaris-dev2dev
> >> _______________________________________________
> >> Nelsonlab-devel mailing list
> >> Nel...@li...
> >> https://lists.sourceforge.net/lists/listinfo/nelsonlab-devel
> >>
> >>
> >
>
>

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
>
>
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Nelsonlab-devel mailing list
> Nel...@li...
> https://lists.sourceforge.net/lists/listinfo/nelsonlab-devel
>
>