[GeneX-dev] Re: some installation feedback and a Curation tool question

[Todd F. P. <tf...@nc...>]

Dear Matthew:

Thank you for your interest in the GeneX System and your feedback. Note
that I have cc'd this message to the Sourceforge developer list. More
experts monitor that list than the ge...@nc... list.

To get the Curation Tool to talk to your server you must start the
Curation Tool and under the file menu select properties. This will launch
a screen with various user-modifiable parameters including the location of
the server. Specifically, the Perl script URLs for control bundle
download, experiment set download and experiment set submit may be
specified. Then select 'SAVE CHANGES' and 'CLOSE'. These changes will be
reflected in the file curation_tool/data/curation_tool.prp.

We will study your comments on the installation and hopefully incorporate
them into the procedure or make changes necessary to avoid similar
problems.

Thanks,
Todd Peterson
NCGR

On Wed, 28 Nov 2001, Matthew Hobbs wrote:

> Hi,
> 
> I am interested in deploying GeneX locally.  Yesterday I managed to get
> the GeneX server going on my system (a PC running Debian Linux 2.4.14)
> and today I downloaded the Curation tool which seems to start OK
> although I haven't used it properly yet.
> 
> As requested...
> 
> > Suggestions
> > ===========
> >
> > Please keep track of things that you didn't understand or weren't
> > explained well and email them directly to us at:
> > ge...@nc...
> >
> ...here are a couple of points:
> 
> i) I was unable to load the test data into a "skeleton" genex database
> until I changed this authentication configuration line in my
> pg_hba.conf file (untouched since my installation of postgres) from:
> 
> local        all                                           peer sameuser
> 
> to:
> local        all                                           trust
> 
> This allowed user  genex to connect without a password which is what
> genex-initdb-latest tries to do first up.
> 
> 
> ii) I encountered these lines at the end of the GeneX server
> installation process:
> 
> 
> NB:  If you haven't done so in a previous installation, you still have
> to:
> 1) add the text from the file [cron.entries] to the appropriate crontab
> (and
>    force a re-read of that crontab) to intitiate the genex_reaper script
> that
>    cleans up the temporary files.  The important lines are:
> # run the reaper 13 minutes after the hour, every hour.
> 13   *      *    *    *    /usr/local/genex/bin/genex_reaper.pl
> # delete files older than 24 hours every 2hours
> 15   0-23/2 *    *    *    find /usr/local/genex/rcluster/var/poqs/jobs
> -name job* -depth -mtime 1 -exec rm -rf {} ; 2> /dev/null
> 
> 2) Add the line:
>         /usr/local/genex/rcluster/bin/queue_master &
>    to your local startup file (ie. /etc/rc.d/rc.local on RedHat)
> 
> 
> but this information really should be said in the installation
> documentation somewhere too I think.
> 
> 
> iii) (This is my main question!) The Curation tool runs, and I have an
> idea of how it should work from the tutorial documents, but I'm not at
> all sure how to use it in conjunction with my own GeneX server rather
> than the NCGR server.  Can you please point me at some documentation or
> give me some advice on how to configure it?   Obviously I want to be
> able to use it to load data into my own installation.
> 
> 
> Thanks,
> 
> 
> Matthew Hobbs
> 
> 
>