Jemboss and Fink package problems

[David Garcia Aristegui]

You need Tomcat and Axis/SOAP to run Jemboss. Look up where emboss is 
installed with fink ( /sw ??? ). To configure Jemboss tu run as 
standalone:

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/standalone.html

MacOS X
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/macosx_server.html

Go to the directory where the script should be run from:
cd EMBOSS-2.x.x/jemboss/utils
Run the install-jemboss-server.sh script.
./install-jemboss-server.sh

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.

HTH,

David.



>Hi all,
>
>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.
>
>Thanks!
>Lorraine
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Lorraine Cavanaugh
>Hughson Lab
>Department of Molecular Biology
>201 Schultz Labs
>Princeton University
>
>lcavanaugh at molbio.princeton.edu
>mayaguezcoqui at fastmail.fm
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