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<div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small;color:rgb(11,83,148)">Dear Sir/Madam</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small;color:rgb(11,83,148)">I'd
like to change the gene ID for "SL.2.5" to " 3 " version. I tried but
failed. It would be kind of you to help me about this issue.</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small;color:rgb(11,83,148)">Thanks in advance</div><font color="#888888"><font color="#888888"><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small;color:rgb(11,83,148)">Javad Karimi</div></font>
</font>
</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 19, 2020 at 1:29 AM Sage Hornung <<a href="mailto:sage.hornung@neogenomics.com">sage.hornung@neogenomics.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I am trying to get ensemble-rest running. I am starting with a VM provided by Ensembl. Its on Ubuntu 20.04 and it has VEP working properly. I can pass ./verify installation and have also ran a few of the test scripts successfully.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I am using the 100 Version of the API and would like to use the human assembly GRCh37<u></u><u></u></p>
<p class="MsoNormal">I have pulled the latest from ensemble-rest on git and flowed the instructions found here
<a href="https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development" target="_blank">
https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development</a><u></u><u></u></p>
<p class="MsoNormal">I am able to get the dev server running but I get this error.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p style="background:white none repeat scroll 0% 0%"><span style="font-size:12pt;color:black">2020/08/18 13:29:19 (1) ReturnError.pm 61> -------------------- EXCEPTION --------------------MSG: ERROR: No root_dir or dir specifiedS TACK Bio::EnsEMBL::VEP::CacheDir::new /home/ensembl/ensembl-api-folder/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:107STACK
Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache <u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I have reinstalled VEP with the script inside /VEP and added the cache files (I did resize my drive to 80GB) but I still get the error.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">My guess is it has something to do with the registry. I have spent some time following the Perl files and tried setting the dir_specified in a few files manually to where my cache files were downloaded unsuccessfully.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I would greatly appreciate and help or suggestions.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank You,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Sage <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b><span style="font-size:14pt;color:rgb(0,74,151)">Sage Hornung</span></b><span style="font-size:14pt;color:rgb(0,74,151)"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:7pt;line-height:12.05pt">
<i><span style="font-size:12pt;color:rgb(0,74,151)">Software Engineer </span></i><span style="font-size:12pt;color:rgb(0,74,151)"><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:12.05pt"><b><span style="color:rgb(66,66,66)">NeoGenomics Laboratories, Inc.</span></b><span style="color:rgb(66,66,66)"><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:12.05pt"><span style="color:rgb(66,66,66)">2131 Faraday Avenue, Carlsbad, CA 92008<u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:12.05pt"><b><span style="color:rgb(66,66,66)">Phone:
</span></b><span style="color:rgb(66,66,66)">760.516.5114<u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:12.05pt"><b><span style="color:rgb(66,66,66)">Cell:
</span></b><span style="color:rgb(66,66,66)">760.755.3930<u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:12.05pt"><a href="mailto:sage.hornung@neogenomics.com" target="_blank">sage.hornung@neogenomics.com</a><u></u><u></u></p>
<p class="MsoNormal" style="margin-bottom:12pt"><a href="http://neogenomics.com/" target="_blank"><span style="color:rgb(0,74,151)">neogenomics.com</span></a><span style="color:rgb(0,74,151)"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:12pt"><a href="http://neogenomics.com/" target="_blank"><span style="color:rgb(91,155,213);text-decoration:none"><img style="width: 1.25in; height: 0.5208in;" id="gmail-m_1338558220732295251Picture_x0020_1" src="cid:17405ac83544cff311" alt="cid:image001.png@01D27B05.09A580E0" width="120" height="50" border="0"></span></a><span style="color:rgb(91,155,213)"><u></u><u></u></span></p>
<p class="MsoNormal"><a href="https://www.linkedin.com/company/neogenomics-laboratories/" target="_blank"><span style="color:rgb(91,155,213);text-decoration:none"><img style="width: 0.3125in; height: 0.3125in;" id="gmail-m_1338558220732295251Picture_x0020_2" src="cid:17405ac83555b16b22" alt="cid:image002.png@01D2789A.338CAE00" width="30" height="30" border="0"></span></a><span style="color:rgb(91,155,213)">
</span><a href="https://twitter.com/NeoGenomics" target="_blank"><span style="color:rgb(91,155,213);text-decoration:none"><img style="width: 0.3125in; height: 0.3125in;" id="gmail-m_1338558220732295251Picture_x0020_3" src="cid:17405ac8355692e333" alt="cid:image003.png@01D2789A.338CAE00" width="30" height="30" border="0"></span></a><span style="color:rgb(91,155,213)"> </span><a href="https://www.youtube.com/channel/UCBa0vLyn1ZO7tW-RyJOrxPA" target="_blank"><span style="color:rgb(91,155,213);text-decoration:none"><img style="width: 0.3125in; height: 0.3125in;" id="gmail-m_1338558220732295251Picture_x0020_4" src="cid:17405ac83557745b44" alt="cid:image004.png@01D2789A.338CAE00" width="30" height="30" border="0"></span></a><span style="color:rgb(31,73,125)"><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><br>Javad Karimi , PhD<br>Entomology Division<br>Department of Plant Protection<br>School of Agriculture<br>Ferdowsi University of Mashhad <br>Mashhad , Iran<br>Alternate email <a href="mailto:jkb@um.ac.ir" target="_blank">jkb@um.ac.ir</a> <<a href="mailto:javadkarimi10@gmail.com" target="_blank">javadkarimi10@gmail.com</a>><br>Tel. ( W.): +98-51- 38 80 58 17 ; Cell : +98-911 17 00 817</div><div><a href="https://www.sciencedirect.com/science/article/pii/S0022201117304445?via%3Dihub" target="_blank"><br> </a><span style="font-family:tahoma,sans-serif;font-size:small;color:rgb(0,0,0)"><b><a href="https://www.sciencedirect.com/science/article/pii/S0022201117304445?via%3Dihub" target="_blank">Microbial insecticides in Iran: History, current status, challenges and perspective</a><br></b></span><font size="2" face="tahoma, sans-serif"><br></font><br></div></div></div></div></div>