This directory contains the source code for the FISH Oracle web application.

Copyright (c) 2009-2014 Malte Mader
Copyright (c) 2009-2014 Center for Bioinformatics, University of Hamburg

SOURCE CODE
-----------

All Java source code is deposited in src/de/unihamburg/zbh/fishoracle.
Following refered to as src/.

src/client/                Client side code which is compiled to JavaScript by
                           the GWT compiler.
src/server/                Server side code containing the servlet services and
                           further classes for processing data or fetching data
                           from and storing data in the databas.

The necessary C source code for drawing genome annotations ist stored in
gt_db_api/.
                
EXTERNAL LIBRARIES
------------------
                           
External libraries are stored in war/Web-inf/lib.

fo_db_api.jar              Library for accessing the FISH Oracle database.
gt_java.jar                Library for accessing the GenomeTools. Used for
                           drawing genome annotations with AnnotationSketch.
jna.jar                    Needed by gt_java.jar to make C calls from java.
javacsv.jar                Library for reading csv files.

mysql-connector-java-5.1.18-bin.JAR MySQL Connector library needed by fo_db_api.

smartgwt.jar               GWT Widget library (version 4.0p) based on
                           SmartClient 9.0.
gwtUpdload.jar             Library to upload files using AJAX.

commons-fileupload-1.2.1.jar,
commons-io-1.4.jar         Libraries needed for server side file upload handling.

CONFIGURATION FILES
------------------

Configuration files for the web application are stored in config/

database.conf              Connection parameters for the Ensembl and FISH Oracle
                           database.
default.conf               Configuration parameters for AnnotationSketch.

BUILDING FISH ORACLE WAR FILE
-----------------------------
In the root directory of source tree, run

  ``ant'war'           to build the war file.
  ``ant clean''        to remove all compiled binaries and war file.

BUILDING GENOMETOOLS FOR FISH ORACLE
------------------------------------

Just run the script ./install_genometools. This will fetch the latest version
of the GenomeTools from Github, merge the codebase with the necessary additions
to fetch and draw genome annotations for FISH Oracle and compile the binaries
automatically.

The resulting lib/libgenometools.so library file can either be copied to your 
/lib or /lib64 (depending on your system architecture) or the systems
$LD_LIBRARY_PATH can be set to the GenomeTools lib/ folder.