Mercurial > repos > mikel-egana-aranguren > ncbo_services
changeset 16:d3d6bdbcf3ea
get_ontology jars included for simpler installation and README updated with installation information for new tools
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Wed, 18 Jan 2012 11:03:34 +0100 |
| parents | 097aa7000159 |
| children | fc4c8a9b3152 |
| files | NCBO_services/README NCBO_services/get_ontology.jar NCBO_services/get_ontology_lib/commons-codec-1.4.jar NCBO_services/get_ontology_lib/commons-logging-1.1.1.jar NCBO_services/get_ontology_lib/httpclient-4.1.2.jar NCBO_services/get_ontology_lib/httpclient-cache-4.1.2.jar NCBO_services/get_ontology_lib/httpcore-4.1.2.jar NCBO_services/get_ontology_lib/httpmime-4.1.2.jar |
| diffstat | 8 files changed, 14 insertions(+), 35 deletions(-) [+] |
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--- 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 @@ + + + +