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annotate install.sh @ 20:46257c870179 draft

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New installation procedure added
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 12:55:08 +0200
parents cc270db37d33
children
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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1 #!/bin/sh
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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3 # Shell script for installing OPPL-Galaxy
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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5 # This script assumes that it is living in galaxy-dist/tools/oppl/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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6 # if that is not the case, simply edit the var $jars bellow
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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8 jars="../../tool-data/shared/jars/"
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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10 cp oppl_galaxy.jar $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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11 cp inference.jar $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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12 cp query.jar $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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13 cp oppl_query.jar $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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14 cp merge.jar $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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16 cp -r FaCT++-linux-v1.5.2 $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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17 cp -r oppl_galaxy_lib $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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18 cp -r inference_lib $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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19 cp -r query_lib $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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20 cp -r oppl_query_lib $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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21 cp -r merge_lib $jars
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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parents: 19
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23 echo 'Now you should edit /galaxy-dist/tool_conf.xml:'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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24 echo ' <section name="Ontology Pre Processor Language" id="oppl">'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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25 echo ' <tool file="oppl/oppl.xml"/>'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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26 echo ' <tool file="oppl/inference.xml"/>'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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27 echo ' <tool file="oppl/query.xml"/>'
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parents: 19
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28 echo ' <tool file="oppl/oppl_query.xml"/>'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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29 echo ' <tool file="oppl/merge.xml"/>'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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30 echo ' </section>'
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 19
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32 # Foreseen feature: directly edit /galaxy-dist/tool_conf.xml with sed or something