# HG changeset patch
# User Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1349699728 -7200
# Node ID ebf11126df7ce4fa42686c84e498091d8a1e7534
# Parent  e2b16720ef25dbeab209cc9d62aa7479b6eb6845
Orain bai

diff -r e2b16720ef25 -r ebf11126df7c README
--- a/README	Mon Oct 08 14:25:04 2012 +0200
+++ b/README	Mon Oct 08 14:35:28 2012 +0200
@@ -1,33 +1,68 @@
+INSTALLATION VIA MERCURIAL (RECOMMENDED)
+========================================
+
+1.- Stop Galaxy.
+
+2.- Move to galaxy-dist/tools/
+
+3.- Clone the OPPL-Galaxy repository with mercurial: 
+
+hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/ncbo_services
+
+3.- Move to galaxy-dist/tools/ncbo_services/ and copy the .jar files to /galaxy-dist/tool-data/shared/jars/
+
+4.- 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/extract.xml"/>
+    <tool file="ncbo_services/get_ontology_view.xml"/>
+    <tool file="ncbo_services/ncbo_annotator.xml"/>
+    <tool file="ncbo_services/ncbo_annotator.xml"/>
+    <tool file="ncbo_services/ncbo_recommender.xml"/>
+  </section>
+
+5.- Start Galaxy.
+
+For updates: 
+
+1.- Stop Galaxy.
+
+2.- Move to galaxy-dist/tools/ncbo_services/
+
+3.- Pull changes and update working copy: 
+
+hg pull
+hg update
+
+4.- Copy any new *.jar file to /galaxy-dist/tool-data/shared/jars/
+
+5.- Only edit /galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
+
+6.- Start Galaxy.
 
 
 
-			=============
-			NCBO Services
-			=============
-
-
-
-INSTALLATION
-============
+MANUAL INSTALLATION (DIRECT DOWNLOAD)
+=====================================
 
 1.- Stop Galaxy.
 
 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
 
-3.- Create directory /galaxy-dist/tools/NCBO_services/
+3.- Create directory /galaxy-dist/tools/ncbo_services/
 
-4.- Copy the .xml files 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/extract.xml"/>
-    <tool file="NCBO_services/get_ontology_view.xml"/>
-    <tool file="NCBO_services/ncbo_annotator.xml"/>
-    <tool file="NCBO_services/ncbo_recommender.xml"/>
-    <tool file="NCBO_services/ncbo_search.xml"/>
-    <tool file="NCBO_services/ncbo_resourceIndex.xml"/>
+  <section name="NCBO services" id="ncbo_services">
+    <tool file="ncbo_services/get_ontology.xml"/>
+    <tool file="ncbo_services/extract.xml"/>
+    <tool file="ncbo_services/get_ontology_view.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.