Jemboss v.alpha1.0 Release

Tim Carver tcarver at
Mon Nov 5 18:23:12 UTC 2001

Announcing Jemboss v.alpha1.0 Release

Jemboss is a graphical user interface to EMBOSS, written in Java. It is
currently being developed at the HGMP-RC by Tim Carver in the EMBOSS
developement team. It is now part of the EMBOSS distribution.

Jemboss is being written to be run either as (i) a client-server
interface or (ii)  standalone and using a local EMBOSS installation.
However, most of the development has been on building a client-server,
to enable access to EMBOSS from remote sites and on PC workstations.

A server has been setup at the a HGMP which is available to registered
users of the HGMP. This enables the user to download the client onto a
PC or unix platform and connect to the HGMP server which runs the
applications. This webpage is currently available at:

Jemboss presents you with a form to assign the input parameters for each

program. Given a sequence, it will work out the values of the input
parameters that are dependent on the sequence attributes. This is done
by a JNI (Java Native Interface) call to the EMBOSS ajax libraries. It
is also being designed to cope with all the inter-dependencies of other
input parameters. (See the note below for compiling EMBOSS to use JNI).

Results are stored on the server and can be re-called. Also, run
information is stored on the server (date of run, command line). If the
application is run interactively then the results are automatically
displayed on the screen. Otherwise a job manager keeps track of all
programs submitted to a batch queue in a Jemboss session.

File system management is provided, both on the users machine locally
and on the server. The files can be dragged from the file tree into the
form. Files can also be opened and displayed from the file manager. More

work is being carried out in this area, to add additional functionality
(e.g. file transfer between local and remote file systems).

Downloading from the CVS:
This is currently only available from the HGMP CVS server. See:

NB:  In downloading from the CVS server, as well as downloading Jemboss,

you are also downloading an inter-release version of EMBOSS which has
not yet been put through the testing procedures.

To configure EMBOSS to use the Java Native Interface in Jemboss a
"--with-java" and "--with-javaos" need to be used, and pointed at the
java1.3 installation. For example:

./configure --enable-warnings --with-pngdriver=/packages/emboss/png

and must not be configured using the --disable-shared configure option.

Known CVS problem:
The xerces.jar file appears to get currupted when added to the server.
So a copy of this jar file has been made available on via anonymous ftp:

which needs to be put in $EMBOSS_ROOT/jemboss/lib.

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