annotate README @ 28:ebf11126df7c draft default tip

Orain bai

INSTALLATION VIA MERCURIAL (RECOMMENDED)
========================================

1.- Stop Galaxy.

2.- Move to galaxy-dist/tools/

3.- Clone the OPPL-Galaxy repository with mercurial: 

hg clone http://[e-mail]/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.



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/

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_annotator.xml"/>
    <tool file="ncbo_services/ncbo_recommender.xml"/>
  </section>

6.- Start Galaxy.



USAGE
=====

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 [e-mail] or
[e-mail].



ACKNOWLEDGEMENTS
================

The work on get_ontology, extract and get_ontology_view is funded by the
Marie Curie Cofund program of the EU, FP7.



COPYRIGHT AND LICENSE
=====================

get_ontology, extract and get_ontology_view are copyright of Mikel
Egaña Aranguren (2012), and they are distributed under a GPL 3 license
(http://www.gnu.org/licenses/)