Mercurial > repos > mikel-egana-aranguren > ncbo_services
changeset 28:ebf11126df7c draft default tip
Orain bai
| author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Mon, 08 Oct 2012 14:35:28 +0200 |
| parents | e2b16720ef25 |
| children | |
| files | README |
| diffstat | 1 files changed, 53 insertions(+), 18 deletions(-) [+] |
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--- 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.