[EMBOSS] Jemboss launch killing cpu

Michael Leong leongmz at gmail.com
Sat May 21 10:05:36 UTC 2005

Grr.. this is bad.
Every jre/os combination drained the cpu.

w2k/jre 1.5, update 2
w2k/jre 1.5, update 3
w2k/jre 1.4.2 update 8
linux/jre 1.5, update 3

Are there another gui cflient equalivent to jemboss (functionality, 
support, etc)



At 02:23 AM 5/21/2005, Alan Bleasby wrote:
>Dear Mike,
>The JWS bug would have affected a linux client but yours looks
>to be a windows one. I assume the CPU-eating is happening on
>the client?
>I'm CCing this to Tim Carver (jemboss author) who, I believe,
>gets back from holiday this weekend. He may be able to help.
>Alan Bleasby
>I'm trying to setup Jemboss on my lan and trying to use the java webstart
>to launch it.  However, on the Jemboss login window, when the progress
>meter reaches about 50%, it locks up and eats all teh cpu.
>Here are the steps at I took to install it:
>untar EMBOSSS 2.10.0
>untar tomcat 5.5.9
>download emboss install script for tomcat 5.5.x
>untar axis 1.2
>mkdir /opt/emboss-data/soap
>chmod 777 /opt/emboss-data/soap
>chmod a+t /opt/emboss-data/soap
>replace install script w/ one for tomcat 5.5.x
>run ./install-jemboss-server.sh
>install options:
>os: linux
>ssl: yes
>port: 8443
>java: jdk v1.5
>unix auth: yes
>tomcat uid: 1000
>auth method: shadow
>embassy pkgs: no
>clustalw: /usr/bin
>primer3_core: <blank>
>auto deploy: yes
>modifed server.xml as told
>got warning about javax.activation.DataHandler and
>javax.mail.internet.MimeMultipart not found
>     chown root /opt/emboss/bin/jembossctl
>     chmod u+s /opt/emboss/bin/jembossctl
>cd /opt/emboss/share/EMBOSS/jemboss/utils
>edit /opt/emboss/share/EMBOSS/jemboss/jnlp/index.html and Jemboss.jnlp to
>proper webserver
>copy /opt/emboss/share/EMBOSS/jemboss/jnlp/* to webserver

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