Hi Jack,
"screen" over Xming didn't help - close of Xming still shuts down biomart
and "screen" (there is no screen to resume).
My server does not block outgoing URL or alike.
But I think I have found it - by looking through the stdouterr logs in
"dist/logs". When I tried to start it with womething like:
/full/path/to/biomart/dist/scripts/biomart-server.sh start
from an arbitrary location, it keeps looking for
./conf/xml/AttributeTableConfig.xml in my current dir (don't find it),
thus complains several "(Unknown Source)". So I had to start it by
1> cd /usr/local/biomart
2> ./dist/scripts/biomart-server.sh start
so that it sees /usr/local/biomart/conf/xml/AttributeTableConfig.xml
Thanks!
Zhiliang
Date: Thu, 19 May 2011 12:01:03 -0400
From: Jack Hsu <jack....@oicr.on.ca>
To: Zhiliang <h...@animalgenome.org>, BioMart Users <users@biomart.org>
Subject: Re: [BioMart Users] (no subject)
Hi Zhiliang,
The "biomart-server.sh stop" command will look at the biomart.pid file inside
dist directory and kill that process. It may be that the process was already
killed but the pid file still remained.
I'm not sure how Xming works, but the "biomart-server.sh start" script should
be launching the BioMart process as a daemon process. You could try running
the script through a "screen", which you can detach from using ^A^D (Ctlr+A,
Ctlr+D), and reattach using "screen -r". This will allow you to resume
previous screen sessions on the Linux server even if your client disconnects.
The "HTTP Error" occurs during querying when an URL source is not accessible
by the BioMart server. Do you have a firewall that prevents access to outside
resources?
-jack
On 11-05-19 9:55 AM, "Zhiliang" <h...@animalgenome.org> wrote:
Thanks to the hard work by the Biomart team - I was able to download the
new Biomart version 0.8 to install and deploy on my RH Linux server...
Everything seems working alright, except that the serve "ram away" a few
times (quitely die). The observations are:
I use Xming to operate remote Biomart GUI on my Windows XP. I can start
the Biomart with "biomart-server.sh" GUI. When done I can close the GUI
I should correct myself - I had a wrong copy/paste here, it should be
"/usr/local/biomart/dist/scripts/martconfigurator.sh" to launch the GUI.
and release the shell to it prompt, and even logout from the shell, while
Biomart is running. However I have to keep my Xming alive in the
background. When I attempt to turn off Xming, it warns:
There are currently 2 clients connected; Shut down these client/server?
If I close Xming on my PC, the Biomart on my remote Linux dies.
I also tried to run the server from the command line, as in:
> /usr/local/biomart/dist/scripts/biomart-server.sh start
Sometimes it complains there is already a biomart running, while
"biomart-server.sh stop" won't really stop it, that I had to kill the
process (it's a short process name, different from normal) to try again.
Sometimes it starts, but I got errors on the http/web:
HTTP Error, problem accessing /.Reason: Cannot find
Any advice please?
Zhiliang
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