[EMBOSS] Installing the Jemboss server

[David Martin]

Has anyone actually managed to do this outside HGMP (oops, RFCGR)?

I have been battling with the install script for a few days with varying
degrees of success.

First issue: It doesn't take into account the additional arguements given
for an EMBOSS install (eg. --bindir= --libdir=) which then break it later.
This is easily fixed with a manual edit.

Second issue: It has problems finding various files. Excerpts from the
install included below with comments
--
java.io.FileNotFoundException:
/site/share/EMBOSS/jemboss/resources/wossname.jar
 (No such file or directory)
        at java.io.FileOutputStream.open(Native Method)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
        at sun.tools.jar.Main.run(Main.java:134)
        at sun.tools.jar.Main.main(Main.java:904)
java.io.FileNotFoundException:
/site/share/EMBOSS/jemboss/resources/resources.ja
r (No such file or directory)
        at java.io.FileOutputStream.open(Native Method)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
        at sun.tools.jar.Main.run(Main.java:134)
        at sun.tools.jar.Main.main(Main.java:904)
--
I had removed /site/share/EMBOSS/jemboss before running the script.
/site/share/EMBOSS/jemboss/resources/ points to the axis web application
directory under tomcat. (axis/WEB-INF/classes/resources)
--
error: cannot read:
/site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss
AuthServer.java
1 error
error: cannot read:
/site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss
FileAuthServer.java
1 error
--
the relevant files have for some reason been installed under
/site/share/EMBOSS/jemboss/org/org/emboss/jemboss/server
by the install script.

and it goes on with many more file not found errors. If these are ignored
then further problems arise later.

..d

-- 
David Martin PhD <david at compbio.dundee.ac.uk>
Post-Genomics and Molecular Interactions Centre
University of Dundee
ICQ: 337640638