Jemboss and Fink package problems
David Garcia Aristegui
david at cnb.uam.es
Tue Apr 22 08:19:24 UTC 2003
You need Tomcat and Axis/SOAP to run Jemboss. Look up where emboss is
installed with fink ( /sw ??? ). To configure Jemboss tu run as
Go to the directory where the script should be run from:
Run the install-jemboss-server.sh script.
Go to the jemboss directory in the EMBOSS install directory
($EMSBOSS_INSTALL/share/EMBOSS/jemboss) and try running Jemboss. Edit
runJemboss.csh to set the following environment variables:
setenv EMBOSS_INSTALL /usr/local/emboss/
setenv LD_LIBRARY_PATH $EMBOSS_INSTALL/lib
For MacOSX also add:
setenv DYLD_LIBRARY_PATH $EMBOSS_INSTALL/lib
Also add the 'local' option for Jemboss to run in 'standalone' mode:
( very important, java1.3 or higher should be used ).
java org/emboss/jemboss/Jemboss local &
Then try running it by typing ./runJemboss.csh.
>I have recently attempted to install Emboss and Jemboss to run in
>standalone mode on my G4 laptop. I was unable to get the program
>suite to compile properly using the Jemboss script, but was able to
>get Fink to install the package for me.
>Anyone have ideas on how to configure Emboss to run as standalone
>with a Jemboss interface with a Fink installation? I think Fink
>only installed Emboss (which works fine from the command line). I
>did install Jemboss, which launches, but asks for a username and
>password on startup, so I think it's trying to run in client mode.
>Department of Molecular Biology
>201 Schultz Labs
>lcavanaugh at molbio.princeton.edu
>mayaguezcoqui at fastmail.fm
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