Final fixes before release

Author: mikessh

README.txt

@@ -2,6 +2,7 @@
 = ONCOFUSE V1.0.9 =
 ===================
 
+
 Oncofuse is a framework designed to estimate the oncogenic potential of de-novo discovered gene fusions. It uses several hallmark features and employs a bayesian classifier to provide the probability of a given gene fusion being a driver mutation.
 
 Oncofuse is described in the following paper:
@@ -10,6 +11,7 @@ Mikhail Shugay, Inigo Ortiz de Mendibil, Jose L. Vizmanos and Francisco J. Novo.
 See http://www.unav.es/genetica/oncofuse.html for further details.
 
 
+
 >WHAT'S NEW
 
 - Version 1.0.9 (Nov-2014) minor improvements, support for hg18, hg19 and hg38 genome assemblies. ALWAYS check the coordinate system
@@ -27,13 +29,15 @@ See http://www.unav.es/genetica/oncofuse.html for further details.
 - As from version 1.0.3, installation of Groovy is not necessary. Input file types and the content of output file have also been improved. 
 
 
+
 >OPTIONS
 
 -p option specifies the number of threads Oncofuse will use
 
 -a option specifies genome assembly version. Allowed values: hg18, hg19 and hg38. Default value: hg19
 
 
+
 >INPUT
 
 This tool is designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. It also provides information on hallmarks of driver gene fusions, such as expression gain of resulting fusion gene, retained protein interaction interfaces and resulting protein domain functional profile.
@@ -65,6 +69,7 @@ input_type = "rnastar"
 Default output file of RNASTAR software. Data is pre-filtered based on number of spanning N>=1 and total number of supporting reads M>=2 reads. These parameters could be changed with extended input type argument "rnastar-N-M". Tissue type has to be set using tissue_type argument.
 
 
+
 >OUTPUT
 
 A tab-delimited table with the following columns

pom.xml

@@ -82,8 +82,15 @@
                                     </fileset>
                                 </copy>
                                 <zip destfile="${project.basedir}/${project.build.finalName}.zip">
-                                    <fileset dir="${project.build.directory}"
-                                             includes="libs/**,common/**,${project.build.finalName}.${project.packaging}"/>
+                                    <zipfileset dir="${project.build.directory}"
+                                                includes="libs/**,common/**,example/**"
+                                                prefix="${project.build.finalName}"/>
+                                    <zipfileset dir="${project.build.directory}"
+                                                includes="${project.build.finalName}.jar"
+                                                fullpath="${project.build.finalName}/Oncofuse.jar"/>
+                                    <zipfileset dir="${project.basedir}"
+                                                includes="README.txt,LICENCE.txt"
+                                                prefix="${project.build.finalName}"/>
                                 </zip>
                             </tasks>
                         </configuration>