running Jemboss after EMBOSS installation

[Fernan Aguero]

+----[ Dr T. Carver <tcarver at hgmp.mrc.ac.uk> (31.Jan.2003 14:55):
|
| Hi Fernan

Hi Tim,

| There is an install script provided in EMBOSS-2.6.0/jemboss/utils, that
| installs EMBOSS and Jemboss (along with Tomcat and Axis if you are doing
| a server installation). It compiles EMBOSS with the --with-java and
| --with-javaos flags and --with-thread=$PLATFORM. The script compiles
| Jemboss and adds the Axis library to Tomcat. It will also deploy the Axis
| (SOAP) methods that Jemboss can access.

I see. Actually I already got there and was trying to make
sense of what the install script did. In the case of a
standalone server, and as far as I can see, the script just
invokes configure, make and make install, passing some extra
arguments, and then goes into running a few commands (java
stuff that I don't understand), and finally producing a
jemboss.properties file.

Now, what if I -- without using the script at all -- try to
build EMBOSS using the same flags, will this produce a
working Jemboss?

I ask this because I want to include Jemboss as an option in
the FreeBSD port. My idea regarding this is to include
functionality from install-jemboss.sh into the Makefile, and
let the users say:

make WITH_JEMBOSS=yes

and have everything dealt with automagically.
This is because many of the other things your script does
(checking for java versions, locations, etc.) are already
dealt with by FreeBSD's included Makefiles (in this case
bsd.java.mk). Thus I need only include a few lines from your
script into the FreeBSD Makefile.

I haven't tested it yet but my Makefile would look like the following
(right now I'm only assuming a standalone Jemboss):

.if defined(WITH_JEMBOSS)
USE_JAVA=               1.3+
CONFIGURE_ARGS+=        --with-java=${JAVA_HOME}/include \
                        --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L}
CONFIGURE_ENV+=					PATH=${PATH}:${JAVA_HOME}/bin
MAKE_ENV+=							PATH=${PATH}:${JAVA_HOME}/bin
.endif

Now JAVA_HOME and JAVA_OS (freebsd) are defined in bsd.java.mk, and
this in turn is included because I defined USE_JAVA.
CONFIGURE_ENV and MAKE_ENV are variables that are passed to
configure and make when they're invoked.

Now, in my post-install target I have (taken from your
script):

.if defined(WITH_JEMBOSS) 
	JEMBOSS=    ${PREFIX}/share/EMBOSS/jemboss
	@ cd ${JEMBOSS} && \
	${PREFIX}/bin/wossname -colon -gui -outf wossname.out -auto
  @ ${JAVA_HOME}/bin/jar cvf ${JEMBOSS}/resources/wossname.jar wossname.out
	@ ${JAVA_HOME}/bin/javac -classpath ${JEMBOSS} ${JEMBOSS}/org/emboss/jemboss/server/JembossServer.java
	@ ${JAVA_HOME}/bin/javac -classpath ${JEMBOSS} ${JEMBOSS}/org/emboss/jemboss/server/JembossFileServer.java
	@ ${SED} -e 's|^#java org|java org|' -e 's|^java org.emboss.jemboss.Jemboss &|#java	org.emboss.jemboss.Jemboss &|' \
	-e 's|^#setenv EMBOSS_INSTALL.*|setenv EMBOSS_INSTALL	$EMBOSS_INSTALL/lib|' \
	-e 's|^#setenv LD_LIBRARY_PATH|setenv LD_LIBRARY_PATH|' \
	${JEMBOSS}/runJemboss.csh
.endif
								
I have yet to include stuff to generate the
jemboss.properties file, but you get the idea.

I'm going to try this and report back, but please share your
opinions. Is there anything I missed? 
I know that this is not the best solution, since everytime
you modify anything to your install script, I need to update
the FreeBSD port. 

Perhaps this could be added to the main EMBOSS Makefile, now
that Jemboss is at 1.0 and is _the_ official GUI?


| If you do a plain EMBOSS installation Jemboss is not installed at all.

What I see is that a plain EMBOSS installation does not
produce a working Jemboss, but it nonetheless installs a
PREFIX/share/EMBOSS/jemboss tree, and some files in
PREFIX/bin. Perhaps this can be avoided in the case of plain
EMBOSS installations?

| Hope this helps.

Indeed it is helping.

Best regards,

Fernan

| 
+----]

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan