# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1326881014 -3600
# Node ID d3d6bdbcf3eadc2c969a405b6ca8692a183a194b
# Parent  097aa7000159b1cd0c0401d006b9df850acef156
get_ontology jars included for simpler installation and README updated with installation information for new tools

diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/README
--- a/NCBO_services/README	Thu Jan 12 10:27:50 2012 +0100
+++ b/NCBO_services/README	Wed Jan 18 11:03:34 2012 +0100
@@ -12,17 +12,19 @@
 
 1.- Stop Galaxy.
 
-2.- Copy the .jar files and _lib/ directories to
-/galaxy-dist/tool-data/shared/jars/
+2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
 
 3.- Create directory /galaxy-dist/tools/NCBO_services/
 
-4.- Copy get_ontology.xml to /galaxy-dist/tools/NCBO_services/
+4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/
 
 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
 
   <section name="NCBO services" id="NCBO_services">
     <tool file="NCBO_services/get_ontology.xml"/>
+    <tool file="NCBO_services/ncbo_annotator.xml"/>
+    <tool file="NCBO_services/ncbo_annotator.xml"/>
+    <tool file="NCBO_services/ncbo_recommender.xml"/>
   </section>
 
 6.- Start Galaxy.
@@ -32,44 +34,17 @@
 USAGE
 =====
 
-A bioportal API key and an ontology id must be provided. The API key can be
-obtained by creating an account at bioportal
-(http://bioportal.bioontology.org/). The id can be obtained in the ontology page
-(e.g. 1522 for BioPAX, see http://bioportal.bioontology.org/ontologies/1522)
+Each tool has a different functionality, but all of them need a
+bioportal API key. The API key can be obtained by creating an account at
+bioportal (http://bioportal.bioontology.org/). 
 
 
 
 CONTACT
 =======
 
-Please send any request or comment to mikel.egana.aranguren@gmail.com.
-
-
-
-ACKNOWLEDGEMENTS
-================
-
-This work is funded by the Marie Curie Cofund program of the EU, FP7.
-
-
-
-COPYRIGHT AND LICENSE
-=====================
-
-Copyright (c) 2011 Mikel Egaña Aranguren. 
-
-NCBO Services is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program 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
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
+Please send any request or comment to mikel.egana.aranguren@gmail.com or
+jose.minya@gmail.com.
 
 
 
@@ -79,3 +54,7 @@
 
 
 
+
+
+
+
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology.jar
Binary file NCBO_services/get_ontology.jar has changed
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology_lib/commons-codec-1.4.jar
Binary file NCBO_services/get_ontology_lib/commons-codec-1.4.jar has changed
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology_lib/commons-logging-1.1.1.jar
Binary file NCBO_services/get_ontology_lib/commons-logging-1.1.1.jar has changed
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology_lib/httpclient-4.1.2.jar
Binary file NCBO_services/get_ontology_lib/httpclient-4.1.2.jar has changed
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology_lib/httpclient-cache-4.1.2.jar
Binary file NCBO_services/get_ontology_lib/httpclient-cache-4.1.2.jar has changed
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology_lib/httpcore-4.1.2.jar
Binary file NCBO_services/get_ontology_lib/httpcore-4.1.2.jar has changed
diff -r 097aa7000159 -r d3d6bdbcf3ea NCBO_services/get_ontology_lib/httpmime-4.1.2.jar
Binary file NCBO_services/get_ontology_lib/httpmime-4.1.2.jar has changed