JEnsembl: JavaAPI to Ensembl Datasources Files

This release version 1.78 contains binary Jars for JEnsembl: the demonstration Ensembl Java API.

It also contains source and javadoc jars for each module - and it contains binary jars for dependencies.

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JEnsembl is a sourceforge-hosted open-source project at https://sourceforge.net/projects/jensembl/

=========================LICENCE==========================================

Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>

This file is part of the Ensembl Java API demonstration project developed by the Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh.

This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License (version 3) as published by the Free Software Foundation.

This software is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License in this software distribution. If not, see <http://www.gnu.org/licenses/gpl-3.0.html/>.

==========================================================================


JEnsembl is a Maven project, and uses the dependency mechanism, but
these binaries allow any Java project to use the compiled libraries.

Java code
_________

Code available by SVN client at
 
svn checkout svn://svn.code.sf.net/p/jensembl/code/ yourdir

or on the web at 

http://sourceforge.net/p/jensembl/code

[ NB: this release is tagged at

svn checkout svn://svn.code.sf.net/p/jensembl/code/tags/jensembl-project-1.78/EnsemblTest  path/to/yourdir

or

http://sourceforge.net/p/jensembl/code/537/tree/tags/jensembl-project-1.78]


For Maven Users etc ....all the required dependencies for the code are available at

central Central Repository http://repo1.maven.org/maven2 and 
biojava-maven-repo BioJava repository  http://www.biojava.org/download/maven/

the jensembl artifacts themselves are now hosted at our maven repository http://jensembl.sourceforge.net/m2-repo


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Demonstration code 

testing and demonstrating the use of these binaries is available at [SVN access]

svn checkout svn://svn.code.sf.net/p/jensembl/code/tags/jensembl-project-1.78/EnsemblTest  path/to/yourdir

or 

http://sourceforge.net/p/jensembl/code/537/tree/tags/jensembl-project-1.78/EnsemblTest/

and is included in this release as : ensembl-test-1.78-sources.jar


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BINARIES

the individual jar/artifacts are available in 

		release1_78.zip (see below)

however, for convenience all of the jensembl binaries and the dependencies (apart from the configuration module) 
are bundled together in

		jensembl-bundle-no-config-1.78.jar

this binary jar requires the presence of a version of the config jar 

		ensembl-config-1.78.jar

this may be replaced with later versions of the config jar as ensembl releases new database versions, as long as no critical alterations to the ensembl schema are mode (requiring updates to the JEnsembl datamapping code).

alternatively, local configuration files may be loaded in onjunction with the config jar. 

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release1_78.zip contents
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ENSEMBL JAVA API (Binary, source and javadoc jars)
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ensembl-config-1.78.jar
ensembl-data-access-1.78.jar
ensembl-data-access-1.78-javadoc.jar
ensembl-data-access-1.78-sources.jar
ensembl-data-access-interface-1.78.jar
ensembl-data-access-interface-1.78-javadoc.jar
ensembl-data-access-interface-1.78-sources.jar
ensembl-datamapper-1.78.jar
ensembl-datamapper-1.78-javadoc.jar
ensembl-datamapper-1.78-sources.jar
ensembl-datasource-aware-model-1.78.jar
ensembl-datasource-aware-model-1.78-javadoc.jar
ensembl-datasource-aware-model-1.78-sources.jar
ensembl-model-1.78.jar
ensembl-model-1.78-javadoc.jar
ensembl-model-1.78-sources.jar


(source code available at 
https://jensembl.svn.sourceforge.net/svnroot/jensembl/tags/jensembl-project-1.78/)

DEMONSTRATION CODE (source and javadoc jars)
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ensembl-test-1.78.jar
ensembl-test-1.78-javadoc.jar
ensembl-test-1.78-sources.jar


(source code available at 
https://jensembl.svn.sourceforge.net/svnroot/jensembl/tags/jensembl-project-1.78/)


BIOJAVA 3 DEPENDENCIES (see http://www.biojava.org/wiki/BioJava3_project )
___________________________________________________________________________

jensembl now uses  release 3.0.3

biojava3-core-3.0.3.jar


        <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava3-core</artifactId>
            <version>3.0.3</version>
        </dependency>

from

biojava-maven-repo BioJava repository http://www.biojava.org/download/maven/

        <repository>
            <id>biojava-maven-repo</id>
            <name>BioJava repository</name>
            <url>http://www.biojava.org/download/maven/</url>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
            <releases>
                <enabled>true</enabled>
                <checksumPolicy>ignore</checksumPolicy>
            </releases>
        </repository>



GENERAL DEPENDENCIES
____________________
     
biojava3-core-3.0.3.jar          

mysql-connector-java-5.1.6.jar
mybatis-3.0.2.jar
cglib-nodep-2.1_3.jar


LOGGING
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slf4j-api-1.6.1.jar
log4j-1.2.16.jar

for 'no logging' include....
slf4j-nop-1.6.1.jar

to activate logging - include...
slf4j-log4j12-1.6.1.jar

or the logger of your choice


readme.txt (this)
GPLv3licence.txt