Mercurial > repos > mikel-egana-aranguren > oppl

annotate README @ 22:8d4bbaa99b4a draft

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Minor changes for JBS paper
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sun, 14 Oct 2012 17:21:51 +0200
parents ffde1fafa066
children
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1 INSTALLATION VIA MERCURIAL (RECOMMENDED)
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2 ========================================
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3
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4 1.- Stop Galaxy.
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5
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6 2.- Move to galaxy-dist/tools/
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8 3.- Clone the OPPL-Galaxy repository with mercurial:
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10 hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/oppl
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12 4.- Move to galaxy-dist/tools/oppl/ and run install.sh:
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14 chmod +x install.sh
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15 ./install.sh
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17 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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19 <section name="Ontology Pre Processor Language" id="oppl">
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20 <tool file="oppl/oppl.xml"/>
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21 <tool file="oppl/inference.xml"/>
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22 <tool file="oppl/query.xml"/>
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23 <tool file="oppl/oppl_query.xml"/>
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24 <tool file="oppl/merge.xml"/>
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25 </section>
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26
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27 6.- Start Galaxy.
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28
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29 For updates:
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30
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31 1.- Stop Galaxy.
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32
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33 2.- Move to galaxy-dist/tools/oppl/
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35 3.- Pull changes and update working copy with mercurial:
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37 hg pull
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38 hg update
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39
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40 4.- Run install.sh:
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41
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42 ./install.sh
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44 5.- Only edit galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
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46 6.- Start Galaxy.
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50 MANUAL INSTALLATION (DIRECT DOWNLOAD)
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51 =====================================
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52
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53 Download and uncompress anywhere you like, and then:
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55 1.- Stop Galaxy.
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57 2.- Copy the following files and directories to
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58 galaxy-dist/tool-data/shared/jars/:
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60 oppl_galaxy_tool.jar
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61 inference.jar
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62 query.jar
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63 oppl_query.jar
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64 merge.jar
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65 oppl_galaxy_lib/
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66 inference_lib/
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67 query_lib/
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68 oppl_query_lib/
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69 merge_lib/
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70 FaCT++-linux-v1.5.2/
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71 FaCT++-OSX-v1.5.2/
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73 3.- Create directory galaxy-dist/tools/oppl/
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75 4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and
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76 merge.xml to galaxy-dist/tools/oppl/
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78 5.- Add the following lines to galaxy-dist/tool_conf.xml:
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80 <section name="Ontology Pre Processor Language" id="oppl">
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81 <tool file="oppl/oppl.xml"/>
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82 <tool file="oppl/inference.xml"/>
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83 <tool file="oppl/query.xml"/>
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84 <tool file="oppl/oppl_query.xml"/>
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85 <tool file="oppl/merge.xml"/>
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86 </section>
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88 6.- Start Galaxy.
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92 FORESEEN FEATURES
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93 =================
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95 - Support for processing ontologies that import other ontologies loaded
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96 in Galaxy (i.e. to resolve imports within galaxy).
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98 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
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100 - OWLLink and Racer support.
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102 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
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103 cell).
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105 - Other output formats apart from RDF/XML.
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107 - Support for DataPropertyAssertion, DataPropertyHierarchy,
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108 DifferentIndividuals, ...
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110 - A new tool for wrapping the ontology modularisation function of the OWL API.
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114 KNOWN BUGS AND ISSUES
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115 =====================
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117 Currently Galaxy interprets any information thrown to stderr as a tool
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118 error, which is bad since OPPL (And many other tools) throw info to
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119 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
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120 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
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121 not fail gracefully (It simply stops). A wrapper will be implemented.
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122
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123 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
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127 CONTACT
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128 =======
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129
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130 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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131
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132
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133
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134 ACKNOWLEDGEMENTS
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135 ================
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136
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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137 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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138
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139
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140
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141 COPYRIGHT AND LICENSE
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142 =====================
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143
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144 Copyright (c) 2011 Mikel Egaña Aranguren.
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145
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146 (OPPL|Inference|Query|OPPL-Query|Merge)-Galaxy
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147 is free software: you can redistribute it and/or modify it under the
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148 terms of the GNU General Public License as published by the Free
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149 Software Foundation, either version 3 of the License, or (at your
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150 option) any later version.
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151
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152 This program is distributed in the hope that it will be useful,
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153 but WITHOUT ANY WARRANTY; without even the implied warranty of
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154 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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155 GNU General Public License for more details.
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156
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157 You should have received a copy of the GNU General Public License
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158 along with this program. If not, see <http://www.gnu.org/licenses/>.
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159
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160 OPPL API, OWL API, Pellet, HermiT, Elk and FaCT++ have their own licenses.
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161
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162