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annotate onto-toolkit/INSTALL @ 1:d2d26d330236

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v 0.2: tools added for OPPL-galaxy
author easr
date Wed, 11 Apr 2012 10:33:41 +0200
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1 INSTALL
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2 =======
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4 ONTO-Toolkit requires:
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6 1. Galaxy (latest version recommended):
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8 http://main.g2.bx.psu.edu/
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10 2. ONTO-PERL (version >= 1.37):
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12 http://search.cpan.org/dist/ONTO-PERL/
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14 After installing the required software:
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16 1. Copy the '/ontology/*.xml' to '$GALAXY_HOME/tools/'
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18 2. Copy the test data file 'pre_cco_core.obo' to '$GALAXY_HOME/test-data/'
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20 3. Adapt your 'tool_conf.xml' file by adding the 'ONTO-ToolKit' section:
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22 <section name="OBO Ontology manipulation" id="ONTO-ToolKit">
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23 <tool file="ontology/get_ancestor_terms.xml"/>
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24 <tool file="ontology/get_child_terms.xml"/>
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25 <tool file="ontology/get_descendent_terms.xml"/>
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26 <tool file="ontology/get_intersection_ontology_from.xml"/>
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27 <tool file="ontology/get_list_intersection_from.xml"/>
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28 <tool file="ontology/get_parent_terms_by_relationship_type.xml"/>
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29 <tool file="ontology/get_parent_terms.xml"/>
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30 <tool file="ontology/get_relationship_types.xml"/>
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31 <tool file="ontology/get_subontology_from.xml"/>
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32 <tool file="ontology/get_terms_by_relationship_type.xml"/>
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33 <tool file="ontology/obo2owl.xml" />
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34 <tool file="ontology/obo2rdf.xml" />
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35 <tool file="ontology/obo2tran.xml" />
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36 <tool file="ontology/term_id_vs_term_def.xml"/>
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37 <tool file="ontology/term_id_vs_term_name.xml"/>
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38 </section>
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39
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40 4. Restart your Galaxy instance.
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41
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42 Bugs/comments/questions/etc
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43 ===========================
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45 ONTO-Toolkit is regularly updated, please report any bugs or
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46 send your comments to erick.antezana -@- gmail.com