<div dir="ltr"><div class="gmail_quote"><div dir="ltr">Hi,<div><br></div><div>I am trying to set up Ensembl website on my system. I followed the given steps on you website to set up Ensembl locally. But there are some problems I am facing while try to run ensembl server.</div><div><br></div><div><div style="font-size:12.8px">My directory structure is :</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">--- /usr/local/ensembl</div><div style="font-size:12.8px"> ---- apache2</div><div style="font-size:12.8px"> ---- ensembl<br></div><div style="font-size:12.8px"><div> ---- bioperl-live</div><div> ---- ensembl-compara</div></div><div style="font-size:12.8px"> ---- ensembl-funcgen</div><div style="font-size:12.8px"> ---- ensembl-git-tools</div><div style="font-size:12.8px"> ---- enesmbl-io</div><div style="font-size:12.8px"> ---- ensembl-orm</div><div style="font-size:12.8px"> ---- ensembl-tools</div><div style="font-size:12.8px"> ---- ensembl-variation</div><div style="font-size:12.8px"> ---- ensembl-webcode</div><div style="font-size:12.8px"> ---- lib</div><div style="font-size:12.8px"> ---- logs</div><div><div style="font-size:12.8px"> ---- public-plugins</div><div style="font-size:12.8px"> ---- tabix</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">If I try "/usr/local/ensembl/apache2/<wbr>bin/httpd -d /usr/local/ensembl" to run server then I got error - </div><div style="font-size:12.8px">that conf folder is not present in /usr/local/ensembl. </div><div style="font-size:12.8px">But conf present in /usr/local/ensembl/ensembl-<wbr>webcode/conf, so I created a soft link to this conf.</div><div style="font-size:12.8px">and again tried to run the same command and also set the modules soft link too.</div><div style="font-size:12.8px">then I got error-</div><div style="font-size:12.8px">------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------</div><div><div><span style="font-size:12.8px"> <span style="background-color:rgb(238,238,238)">Starting up as non-mirror machine</span></span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)"> Server has identities</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)"><br></span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)">##############################<wbr>##############################<wbr>##################</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)"># Species "Homo_sapiens" not defined in ENSEMBL_SPECIES_ALIASES</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)">##############################<wbr>##############################<wbr>##################</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)">##############################<wbr>##############################<wbr>##################</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)"># Species "" not defined in ENSEMBL_SPECIES_ALIASES</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)">##############################<wbr>##############################<wbr>##################</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)"> Starting up Ensembl server on host: <a href="http://scsor0006085001.rtp.openenglab.netapp.com" target="_blank">scsor0006085001.rtp.<wbr>openenglab.netapp.com</a></span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)"><br></span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)">Syntax error on line 152 of /usr/local/ensembl/conf/httpd.<wbr>conf:</span></div><div><span style="font-size:12.8px;background-color:rgb(238,238,238)">Unknown type 'CODE' for directive PidFile at /usr/local/lib/perl/5.18.2/<wbr>Apache2/PerlSections.pm line 198.\n</span></div></div><div style="font-size:12.8px">------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-------------------</div></div></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">And if I try to run "/usr/local/ensembl/ensembl-<wbr>webcode/ctrl-scripts/restart_<wbr>server -r" then again it shows some error -</div><div style="font-size:12.8px">------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-------------</div><div style="font-size:12.8px"><span class="m_-8399169885856182893gmail-im" style="font-size:12.8px"><font face="courier new, courier, monospace"><span style="font-size:12.8px;background-color:rgb(204,204,204)">Syntax error on line 152 of /usr/local/ensembl/ensembl-web<wbr>code/conf/httpd.conf:</span></font></span><div style="color:rgb(0,0,0);font-size:12.8px"><font face="courier new, courier, monospace"><span style="font-size:12.8px;background-color:rgb(204,204,204)">panic: sv_setpvn called with negative strlen -1 at /usr/local/ensembl/ensembl/mod<wbr>ules/Bio/EnsEMBL/Utils/Excepti<wbr><a href="http://on.pm">on.pm</a> line 421.\n</span></font></div><span class="m_-8399169885856182893gmail-im" style="font-size:12.8px"><div><font face="courier new, courier, monospace"><span style="font-size:12.8px;background-color:rgb(204,204,204)"> Could not start server: No such file or directory.</span></font></div><div><font face="courier new, courier, monospace"><span style="font-size:12.8px;background-color:rgb(204,204,204)">[FATAL] Server start failed.</span></font></div><div><font face="courier new, courier, monospace"><span style="font-size:12.8px">------------------------------<wbr>------------------------------<wbr>---------</span></font></div><div><font face="courier new, courier, monospace"><span style="font-size:12.8px"><br></span></font></div><div>And one thing it shows that **host.httpd.pid" file is not there in logs folder.</div><div><br></div><div>And what is the correct command to run ensembl-server ?</div><div>1. /usr/local/ensembl/apache2/<wbr>bin/httpd -d /usr/local/ensembl ( do I have to make softlink ?)</div><div>2. <span style="font-size:12.8px"> </span><span style="font-size:12.8px">/usr/local/ensembl/<wbr>apache2/bin/httpd -d /usr/local/ensembl/ensembl-<wbr>webcode</span></div><div>3. /usr/local/ensembl/ensembl-<wbr>webcode/ctrl-scripts/restart_<wbr>server -r</div><div><br></div><div>Kindly help me to solve it.</div><div><br></div><div>Thanks </div><span class="HOEnZb"><font color="#888888"><div>Manoj</div></font></span></span></div></div>
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