https://wiki.biouml.org/index.php?action=history&feed=atom&title=BioUML_server_installation 2026-04-12T18:57:41Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=9900&oldid=prev 2022-04-18T03:47:46Z

<p></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 03:47, 18 April 2022</td> </tr><tr><td colspan="2" class="diff-lineno">Line 128:</td> <td colspan="2" class="diff-lineno">Line 128:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Logging ===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Logging ===</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.</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;">Sometimes web-related logs are getting to catalina.*.log.</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;">To have only one log file LOGGING_MANAGER=&quot;-Djava.util.logging.manager=java.util.logging.LogManager&quot; should be passed to catalina properties.</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>== Compilation ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Compilation ==</div></td></tr> </table>

Anna@developmentontheedge.com https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=7536&oldid=prev 2017-05-18T07:18:37Z

<p>‎<span dir="auto"><span class="autocomment">Getting sources</span></span></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 07:18, 18 May 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 51:</td> <td colspan="2" class="diff-lineno">Line 51:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Getting sources ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Getting sources ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Request an account via e-mail to developers, then:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Request an account via e-mail to developers, then:</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>git clone http://gitlab.dote.ru/isb/biouml.git BioUML</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>git clone http://gitlab.dote.ru/isb/graph.git Graph</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins>git clone http://gitlab.dote.ru/isb/biouml.git BioUML</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 class="diffchange diffchange-inline">&#160; </ins>git clone http://gitlab.dote.ru/isb/graph.git Graph</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>== Deployment prepare ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Deployment prepare ==</div></td></tr> </table>

Ivan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=7535&oldid=prev 2017-05-18T07:18:00Z

<p>‎<span dir="auto"><span class="autocomment">Getting sources</span></span></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 07:18, 18 May 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 50:</td> <td colspan="2" class="diff-lineno">Line 50:</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>== Getting sources ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Getting sources ==</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">CVS: use the following CVS</del>-<del class="diffchange diffchange-inline">root</del>:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Request an account via e</ins>-<ins class="diffchange diffchange-inline">mail to developers, then</ins>:</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>:<del class="diffchange diffchange-inline">pserver:&lt;username&gt;@cvs</del>.<del class="diffchange diffchange-inline">developmentontheedge</del>.<del class="diffchange diffchange-inline">com:</del>/<del class="diffchange diffchange-inline">usr</del>/<del class="diffchange diffchange-inline">cvsroot-</del>biouml <del class="diffchange diffchange-inline">(please request an account via e-mail)</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">git clone http</ins>:<ins class="diffchange diffchange-inline">//gitlab</ins>.<ins class="diffchange diffchange-inline">dote</ins>.<ins class="diffchange diffchange-inline">ru</ins>/<ins class="diffchange diffchange-inline">isb</ins>/biouml<ins class="diffchange diffchange-inline">.git BioUML</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 class="diffchange diffchange-inline">git clone http://gitlab.dote.ru/isb/graph.git Graph</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>== Deployment prepare ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Deployment prepare ==</div></td></tr> </table>

Ivan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=6784&oldid=prev 2016-05-30T10:41:04Z

<p>‎<span dir="auto"><span class="autocomment">Prerequisites</span></span></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 10:41, 30 May 2016</td> </tr><tr><td colspan="2" class="diff-lineno">Line 22:</td> <td colspan="2" class="diff-lineno">Line 22:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Eclipse Java IDE (preferred IDE for development, you may use others as well).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Eclipse Java IDE (preferred IDE for development, you may use others as well).</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;">* Microsoft fonts</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;">&#160; apt-get install msttcorefonts</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;">&#160; fc-cache -fv</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>== BioStore server registration ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== BioStore server registration ==</div></td></tr> </table>

Ivan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=6208&oldid=prev 2015-06-25T09:43:55Z

<p>‎<span dir="auto"><span class="autocomment">Development installation</span></span></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 09:43, 25 June 2015</td> </tr><tr><td colspan="2" class="diff-lineno">Line 40:</td> <td colspan="2" class="diff-lineno">Line 40:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; jdbcUser=bioumlsupport2</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; jdbcUser=bioumlsupport2</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; jdbcPassword=bioumlsupport2</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; jdbcPassword=bioumlsupport2</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><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;"><div>&#160; securityProvider=ru.biosoft.access.security.TestSecurityProvider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; securityProvider=ru.biosoft.access.security.TestSecurityProvider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; products=Server;Import;R;Experimental</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; products=Server;Import;R;Experimental</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=6207&oldid=prev 2015-06-25T09:43:39Z

<p>Development installation</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 09:43, 25 June 2015</td> </tr><tr><td colspan="2" class="diff-lineno">Line 32:</td> <td colspan="2" class="diff-lineno">Line 32:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* We will create the server entry and change the permission settings, so you will be able to administer the server.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* We will create the server entry and change the permission settings, so you will be able to administer the server.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Further there will be special form for automated server registration via Biostore</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Further there will be special form for automated server registration via Biostore</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;">== Development installation ==</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;">For internal development installation you may skip the BioStore integration. Instead write the following in the security.properties file:</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;"> jdbcDriverClass=org.gjt.mm.mysql.Driver</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;"> jdbcURL=jdbc:mysql://lachesis:3306/bioumlsupport2</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;"> jdbcUser=bioumlsupport2</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;"> jdbcPassword=bioumlsupport2</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;"> securityProvider=ru.biosoft.access.security.TestSecurityProvider</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;"> products=Server;Import;R;Experimental</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;">This will bypass the authentication and authorization: every user with any password will have administrative privileges and subscription to the specified products. 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Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=6206&oldid=prev 2015-06-16T08:55:40Z

<p>‎<span dir="auto"><span class="autocomment">Prerequisites</span></span></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 08:55, 16 June 2015</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>== Prerequisites ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Prerequisites ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Linux server. Ubuntu preferred.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Linux server. Ubuntu preferred.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Java. Oracle JDK 1.<del class="diffchange diffchange-inline">7 </del>or OpenJDK 1.<del class="diffchange diffchange-inline">7</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Java. Oracle JDK 1.<ins class="diffchange diffchange-inline">8 </ins>or OpenJDK 1.<ins class="diffchange diffchange-inline">8</ins>.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Apache Tomcat (<del class="diffchange diffchange-inline">6</del>+).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Apache Tomcat (<ins class="diffchange diffchange-inline">7</ins>+).</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; aptitude install <del class="diffchange diffchange-inline">tomcat6</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; aptitude install <ins class="diffchange diffchange-inline">tomcat7</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Apache Ant.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Apache Ant.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; aptitude install ant</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; aptitude install ant</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=6205&oldid=prev 2015-06-16T08:55:21Z

<p>‎<span dir="auto"><span class="autocomment">Security properties</span></span></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 08:55, 16 June 2015</td> </tr><tr><td colspan="2" class="diff-lineno">Line 103:</td> <td colspan="2" class="diff-lineno">Line 103:</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>=== Security properties ===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Security properties ===</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* <del class="diffchange diffchange-inline">Enable everything in </del>/usr/lib/jvm/java-<del class="diffchange diffchange-inline">6</del>-<del class="diffchange diffchange-inline">sun</del>/jre/lib/security/java.policy <del class="diffchange diffchange-inline">(</del>or the corresponding file in your Java installation):</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">Add the following line into policy file ( </ins>/usr/lib/jvm/java-<ins class="diffchange diffchange-inline">8</ins>-<ins class="diffchange diffchange-inline">oracle</ins>/jre/lib/security/java.policy or the corresponding file in your Java installation ) <ins class="diffchange diffchange-inline">grant section</ins>:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; grant {</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; grant {</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;&#160; permission <del class="diffchange diffchange-inline">java</del>.<del class="diffchange diffchange-inline">security</del>.<del class="diffchange diffchange-inline">AllPermission</del>;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;&#160; permission <ins class="diffchange diffchange-inline">javax</ins>.<ins class="diffchange diffchange-inline">management</ins>.<ins class="diffchange diffchange-inline">MBeanTrustPermission &quot;register&quot;</ins>;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; };</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; };</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Enable everything in tomcat policy: $CATALINA_HOME/conf/catalina.policy (or policy.d): in the same way.</del></div></td><td colspan="2">&#160;</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>=== Logging ===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Logging ===</div></td></tr> </table>

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<p>JDK 1.7</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 11:24, 5 March 2014</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>== Prerequisites ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Prerequisites ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Linux server. Ubuntu preferred.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Linux server. Ubuntu preferred.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Java. Oracle JDK 1.<del class="diffchange diffchange-inline">6 preferred, but </del>OpenJDK <del class="diffchange diffchange-inline">1.6 and Oracle Java </del>1.7 <del class="diffchange diffchange-inline">also work</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Java. Oracle JDK 1.<ins class="diffchange diffchange-inline">7 or </ins>OpenJDK 1.7.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Apache Tomcat (6+).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Apache Tomcat (6+).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; aptitude install tomcat6</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; aptitude install tomcat6</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server_installation&diff=5150&oldid=prev 2013-09-05T07:34:02Z

<p></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 07:34, 5 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; aptitude install ant-apache-regexp</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; aptitude install ant-apache-regexp</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* MySQL (5+):</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* MySQL (5+):</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; aptitude install mysql-server<del class="diffchange diffchange-inline">-5.1</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; aptitude install mysql-server</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* R (required for some functions such as microarray data normalization) — see [[R installation]] page.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* R (required for some functions such as microarray data normalization) — see [[R installation]] page.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)</div></td></tr> </table>

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