From 730c27c40b7090b9a458e1171993e2ea4b4e9272 Mon Sep 17 00:00:00 2001
From: ted Liefeld <liefeld@broadinstitute.org>
Date: Wed, 19 Jul 2023 12:35:53 -0700
Subject: [PATCH] Trying to make it buildable by Jenkins

---
 build.xml | 53 +++++++++++++++++++++++++++++++++++++++--------------
 manifest  |  4 ++--
 2 files changed, 41 insertions(+), 16 deletions(-)

diff --git a/build.xml b/build.xml
index b12c202..47e87b8 100644
--- a/build.xml
+++ b/build.xml
@@ -1,18 +1,43 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project basedir="." default="create-zip" name="NearestTemplatePrediction">
-	<property name="dirOffset" value="../"/>
-	<import file="${dirOffset}/commontargets.xml"/>
+<!--
+  The Broad Institute
+  SOFTWARE COPYRIGHT NOTICE AGREEMENT
+  The MIT License (MIT)
 
-	<target name="create-zip" depends="init">
-		<antcall target="prezip"/>
-		<zip destfile="${dest.dir}/${ant.project.name}.zip" whenempty="fail" defaultexcludes="true">
-			<fileset dir="." includes="manifest, doc.html" excludes="gpunit/**" />
-            <fileset dir="gpunit" includes="*.yml"/>
-			<fileset dir="src">
-				<include name="*.R"/>
-			</fileset>
-		</zip>
-		<antcall target="postzip"/>
-	</target>
+  Copyright (c) 2018-2023 The Regents of the University of California and
+  the Broad Institute of Harvard and MIT
+   
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+    
+  The above copyright notice and this permission notice shall be included in
+  all copies or substantial portions of the Software.
+  
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+  THE SOFTWARE.
+-->
+<project basedir="" default="create-zip" name="NearestTemplatePrediction">
+<property name="dirOffset" value="../common_module_code" />
+<import file="${dirOffset}/commontargets.xml" />
+
+<target name="create-zip" depends="init">
+    <antcall target="prezip"/>
+    <zip destfile="${dest.dir}/${ant.project.name}.zip" whenempty="fail" defaultexcludes="true">
+        <fileset dir="." includes="manifest, paramgroups.json, LICENSE, Dockerfile"/>
+        <fileset dir="." includes="*.sh"/>
+        <fileset dir="." includes="*.html"/>
+        <fileset dir="." includes="*.R"/>
+    </zip>
+    <antcall target="postzip"/>
+</target>
 
 </project>
diff --git a/manifest b/manifest
index 3d45564..9339d40 100644
--- a/manifest
+++ b/manifest
@@ -9,7 +9,7 @@ fileFormat=gct;png;txt;xls;cls
 language=R-3.1.3
 name=NearestTemplatePrediction
 os=any
-
+documentationUrl=https://www.genepattern.org/modules/docs/NearestTemplatePrediction/4#gsc.tab=0
 p1_MODE=IN
 p1_TYPE=FILE
 p1_default_value=
@@ -95,4 +95,4 @@ requiredPatchURLs=
 serializedModel=
 taskType=Prediction
 userid=hoshida@broad.mit.edu
-version=Updated to use R-3.1 and added HTML documentation.
\ No newline at end of file
+version=Updated to use R-3.1 and added HTML documentation.