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--></style><title>Re: Jemboss and Fink package
problems</title></head><body>
<div><font face="Arial" size="+2">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:</font></div>
<div><font face="Arial" size="+2"><br></font></div>
<div><font face="Arial" size="+2"
color="#000000"
>http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/standalone<span
></span>.html</font></div>
<div><font face="Arial" size="+2"><br></font></div>
<div><font face="Arial" size="+2">MacOS X</font></div>
<div><font face="Arial" size="+2"
color="#000000"
>http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/macosx_ser<span
></span>ver.html</font></div>
<div><font face="Arial" size="+2"><br></font></div>
<div><font face="Arial" size="+2" color="#000000">Go to the directory
where the script should be run from:</font></div>
<div><font face="Arial" size="+2" color="#000000">cd
EMBOSS-2.x.x/jemboss/utils<br>
Run the install-jemboss-server.sh script.</font></div>
<div><font face="Arial" size="+2"
color="#000000">./install-jemboss-server.sh</font></div>
<div><font face="Arial" size="+2" color="#000000"><br></font></div>
<div><font face="Arial" size="+2" color="#000000">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:<br>
<br>
setenv EMBOSS_INSTALL /usr/local/emboss/</font></div>
<div><font face="Arial" size="+2" color="#000000">setenv
LD_LIBRARY_PATH $EMBOSS_INSTALL/lib</font></div>
<div><font face="Arial" size="+2" color="#000000"><br>
For MacOSX also add:</font></div>
<div><font face="Arial" size="+2" color="#000000">setenv
DYLD_LIBRARY_PATH $EMBOSS_INSTALL/lib</font></div>
<div><font face="Arial" size="+2" color="#000000"><br>
Also add the 'local' option for Jemboss to run in 'standalone'
mode:</font></div>
<div><font face="Arial" size="+2" color="#000000">( very important,<b>
java1.3 or higher should be used</b> ).</font></div>
<div><font face="Arial" size="+2" color="#000000"><b>java
org/emboss/jemboss/Jemboss local &</b><br>
<br>
Then try running it by typing ./runJemboss.csh.</font></div>
<div><font face="Arial" size="+2" color="#000000"><br></font></div>
<div><font face="Arial" size="+2" color="#000000">HTH,</font></div>
<div><font face="Arial" size="+2" color="#000000"><br></font></div>
<div><font face="Arial" size="+2" color="#000000">David.</font><font
face="Lucida Grande" size="+2" color="#000000"><br>
</font></div>
<div><br></div>
<div><br></div>
<blockquote type="cite" cite>Hi all,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Thanks!<br>
Lorraine<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
Lorraine Cavanaugh<br>
Hughson Lab<br>
Department of Molecular Biology<br>
201 Schultz Labs<br>
Princeton University<br>
<br>
lcavanaugh@molbio.princeton.edu<br>
mayaguezcoqui@fastmail.fm</blockquote>
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