https://wiki.biouml.org/index.php?action=history&feed=atom&title=GO_installation 2026-04-13T01:18:50Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=GO_installation&diff=4919&oldid=prev 2013-07-15T09:45:25Z

<p>+MySQL packet size info</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:45, 15 July 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Notes ===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Notes ===</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#You may experience the problems with mysql packet size. See http://dev.mysql.com/doc/refman/5.0/en/packet-too-large.html for details.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#Lucene indexes should be created separately for installed GO. See [[Lucene indexes creation]] for details.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#Lucene indexes should be created separately for installed GO. See [[Lucene indexes creation]] for details.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Installation]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Installation]]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=GO_installation&diff=4343&oldid=prev 2013-06-11T11:05:23Z

<p>s/Ensembl/GO/</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:05, 11 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Notes ===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Notes ===</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#Lucene indexes should be created separately for installed <del class="diffchange diffchange-inline">Ensembl</del>. See [[Lucene indexes creation]] for details.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#Lucene indexes should be created separately for installed <ins class="diffchange diffchange-inline">GO</ins>. See [[Lucene indexes creation]] for details.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Installation]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Installation]]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=GO_installation&diff=4342&oldid=prev 2013-06-11T11:05:10Z

<p>+Lucene indexes info</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:05, 11 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This page describes how to install Gene onthology database and integrate it with [[BioUML server]] or [[BioUML workbench]].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This page describes how to install <ins class="diffchange diffchange-inline">or update </ins>Gene onthology database and integrate it with [[BioUML server]] or [[BioUML workbench]].</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Download database dump from GO ftp: &lt;code&gt;&lt;nowiki&gt;ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz&lt;/nowiki&gt;&lt;/code&gt;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Download database dump from GO ftp: &lt;code&gt;&lt;nowiki&gt;ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz&lt;/nowiki&gt;&lt;/code&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** DB_HOST, USER, PASS, DATABASE: mysql database to install into (will drop any existing database with the same name and recreate it; make sure that USER/PASS has all privileges to that database).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** DB_HOST, USER, PASS, DATABASE: mysql database to install into (will drop any existing database with the same name and recreate it; make sure that USER/PASS has all privileges to that database).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Run ant (with default target “install”)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Run ant (with default target “install”)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">=== Notes ===</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#Lucene indexes should be created separately for installed Ensembl. See [[Lucene indexes creation]] for details.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Installation]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Installation]]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=GO_installation&diff=2588&oldid=prev 2013-05-07T05:19:13Z

<p>Links</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:19, 7 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This page describes how to install Gene onthology database and integrate it with BioUML server or BioUML workbench</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This page describes how to install Gene onthology database and integrate it with <ins class="diffchange diffchange-inline">[[</ins>BioUML server<ins class="diffchange diffchange-inline">]] </ins>or <ins class="diffchange diffchange-inline">[[</ins>BioUML workbench<ins class="diffchange diffchange-inline">]].</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Download database dump from GO ftp: &lt;code&gt;&lt;nowiki&gt;ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz&lt;/nowiki&gt;&lt;/code&gt;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Download database dump from GO ftp: &lt;code&gt;&lt;nowiki&gt;ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz&lt;/nowiki&gt;&lt;/code&gt;</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=GO_installation&diff=18&oldid=prev 2013-03-28T05:30:38Z

<p>Created page with &quot;This page describes how to install Gene onthology database and integrate it with BioUML server or BioUML workbench * Download database dump from GO ftp: &lt;code&gt;&lt;nowiki&gt;ftp://f...&quot;</p> <p><b>New page</b></p><div>This page describes how to install Gene onthology database and integrate it with BioUML server or BioUML workbench<br /> <br /> * Download database dump from GO ftp: &lt;code&gt;&lt;nowiki&gt;ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz&lt;/nowiki&gt;&lt;/code&gt;<br /> * Go to BioUML src directory/db_setup/GO<br /> * Edit build.xml there:<br /> ** INPUT_DIRECTORY: where DB dump is located<br /> ** FILE_NAME: name of DB dump<br /> ** TARGET_PATH: $SERVER_PATH/repo<br /> ** DB_HOST, USER, PASS, DATABASE: mysql database to install into (will drop any existing database with the same name and recreate it; make sure that USER/PASS has all privileges to that database).<br /> * Run ant (with default target “install”)<br /> <br /> [[Category:Installation]]</div>

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