Mercurial > repos > erick-antezana > onto-toolkit

annotate onto-toolkit/INSTALL @ 0:4484575e4186

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author erick-antezana
date Tue, 07 Jun 2011 17:51:45 -0400
parents
children d2d26d330236
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
1 INSTALL
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
2 =======
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
3
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
4 ONTO-Toolkit requires:
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
5
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
6 1. Galaxy (latest version recommended):
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
7
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
8 http://main.g2.bx.psu.edu/
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
9
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
10 2. ONTO-PERL (version >= 1.18):
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
11
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
12 http://search.cpan.org/dist/ONTO-PERL/
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
13
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
14 After installing the required software:
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
15
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
16 1. Copy the '/ontology/*.xml' to '$GALAXY_HOME/tools/'
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
17
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
18 2. Copy the test data file 'pre_cco_core.obo' to '$GALAXY_HOME/test-data/'
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
19
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
20 3. Adapt your 'tool_conf.xml' file by adding the 'ONTO-ToolKit' section:
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
21
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
22 <section name="OBO Ontology manipulation" id="ONTO-ToolKit">
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
23 <tool file="ontology/get_ancestor_terms.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
24 <tool file="ontology/get_parent_terms.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
25 <tool file="ontology/get_descendent_terms.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
26 <tool file="ontology/get_child_terms.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
27 <tool file="ontology/term_id_vs_term_def.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
28 <tool file="ontology/term_id_vs_term_name.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
29 <tool file="ontology/get_relationship_types.xml"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
30 <tool file="ontology/obo2rdf.xml" />
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
31 <tool file="ontology/obo2tran.xml" />
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
32 <tool file="ontology/obo2owl.xml" />
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
33 </section>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
34
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
35 4. Restart your Galaxy instance.
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
36
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
37 Bugs/comments/questions/etc
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
38 ===========================
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
39
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
40 ONTO-Toolkit is regularly updated, please report any bugs or
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
41 send your comments to erick.antezana -@- gmail.com