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<p class="MsoNormal">Hi, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for the suggestion on modifying the <Controller::VEP> section. This got me to a different error but I guess I should have fully explained what I am trying to do.
<o:p></o:p></p>
<p class="MsoNormal">I am currently loading a MySQL database with all the homo_sapien GRCh37 data (Almost done this is taking a while. The big tables have taken a few days each)<o:p></o:p></p>
<p class="MsoNormal">I want to point the REST instance I am currently setting up to our instance of the CRCh37 database once its ready.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So while I am waiting for the data to load I would like to set up the ensemble-rest as close as possible to the final configuration.
<o:p></o:p></p>
<p class="MsoNormal">This would mean calling the database instead of using the cache files.
<o:p></o:p></p>
<p class="MsoNormal">It would be great if I could make a couple small calls to the ensemble DB using the rest interface
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It seems as if I can add any configurations to ensembl_rest.conf found here <a href="https://uswest.ensembl.org/info/docs/tools/vep/script/vep_options.html">https://uswest.ensembl.org/info/docs/tools/vep/script/vep_options.html</a> to
the section of the <Controller::VEP> and they should be passed to vep <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">There is also a section at the top of the ensembl_rest.conf<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So have changed these sections a bit I added the database flag to <Controller::VEP> and tried adding the port and host to <Controller::VEP> but it is still not working<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p><span style="font-size:12.0pt;color:black">Model::Registry><br>
###### Database settings. Use if you want to connect to a single database instance. Common options are given below<br>
host = ensembldb.ensembl.org<br>
port = 3337<br>
user = anonymous<br>
<br>
version = 100<br>
verbose = 1<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p><span style="font-size:12.0pt;color:black"><Controller::VEP><br>
fasta = Homo_sapiens.GRCh37.75.dna.toplevel.fa # path to Human toplevel fasta file<br>
# Default parameters for running vep<br>
cache_region_size = 1000000<br>
chunk_size = 50000<br>
whole_genome = 1<br>
compress = gzip -dc<br>
terms = SO<br>
cache = 0<br>
#merged = 0 <br>
failed = 0<br>
core_type = core<br>
quiet = 1<br>
sift = b<br>
polyphen = b<br>
symbol = 1<br>
regulatory = 1<br>
biotype = 1<br>
rest = 1<br>
check_existing = 1 # adds some performance penalty, mitigated by tabix-converting the cache (<a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#convert">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#convert</a>)<br>
fork = 3<br>
max_post_size = 1000<br>
warning_file = STDERR # controls VEP logging, not Catalyst<br>
plugin_config = # path to plugin config<br>
dir_plugins = # path to VEP_plugins checkout<br>
#dir = /home/ensembl/.vep/homo_sapiens/100_GRCh37<br>
database = 1<br>
#host = ensembldb.ensembl.org<br>
#port = 3337<br>
#assebbly = GRCh37<br>
#user = anonymous<br>
</Controller::VEP><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I still get this error <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">The VEP can read gene data from either a local cache or local/remote databases.<br>
<br>
Using a cache is the fastest and most efficient way to use the VEP. The<br>
included INSTALL.pl script can be used to fetch and set up cache files from the<br>
Ensembl FTP server. Simply run "perl INSTALL.pl" and follow the instructions, or<br>
see the documentation pages listed below.<br>
<br>
If you have already set up a cache, use "--cache" or "--offline" to use it.<br>
<br>
It is possible to use the public databases hosted at ensembldb.ensembl.org, but<br>
this is slower than using the cache and concurrent and/or long running VEP jobs<br>
can put strain on the Ensembl servers, limiting availability to other users.<br>
<br>
To enable using databases, add the flag "--database".<br>
<br>
Documentation<br>
Installer: <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer">
http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer</a><br>
Cache: <a href="http://www.ensembl.org/info/docs/tools/vep/script/index.html#cache">
http://www.ensembl.org/info/docs/tools/vep/script/index.html#cache</a><br>
<br>
at /home/ensembl/ensembl-api-folder/ensembl-vep/modules/Bio/EnsEMBL/VEP/Config.pm line 686.<br>
<br>
2020/08/19 13:40:22 (6) Serialize.pm 51> Serializing with Catalyst::Action::Serialize::JSON::XS
<br>
2020/08/19 13:40:22 (1) Catalyst.pm 2726> Response Code: 400; Content-Type: application/json; Content-Length: unknown</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for the assistance<o:p></o:p></p>
<p class="MsoNormal">Sage<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-line-height-alt:12.05pt;text-autospace:none"><b><span style="font-size:14.0pt;color:#004A97">Sage Hornung</span></b><span style="font-size:14.0pt;color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.0pt;line-height:12.05pt;text-autospace:none">
<i><span style="font-size:12.0pt;color:#004A97">Software Engineer </span></i><span style="font-size:12.0pt;color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><b><span style="color:#424242">NeoGenomics Laboratories, Inc.</span></b><span style="color:#424242"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><span style="color:#424242">2131 Faraday Avenue, Carlsbad, CA 92008<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><b><span style="color:#424242">Phone:
</span></b><span style="color:#424242">760.516.5114<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><b><span style="color:#424242">Cell:
</span></b><span style="color:#424242">760.755.3930<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><a href="mailto:sage.hornung@neogenomics.com">sage.hornung@neogenomics.com</a><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><a href="http://neogenomics.com/"><span style="color:#004A97">neogenomics.com</span></a><span style="color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><a href="http://neogenomics.com/"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="120" height="50" style="width:1.25in;height:.5208in" id="Picture_x0020_1" src="cid:image001.png@01D6762B.BCF20FE0" alt="cid:image001.png@01D27B05.09A580E0"></span></a><span style="color:#5B9BD5"><o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://www.linkedin.com/company/neogenomics-laboratories/"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="30" height="30" style="width:.3125in;height:.3125in" id="Picture_x0020_2" src="cid:image002.png@01D6762B.BCF20FE0" alt="cid:image002.png@01D2789A.338CAE00"></span></a><span style="color:#5B9BD5">
</span><a href="https://twitter.com/NeoGenomics"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="30" height="30" style="width:.3125in;height:.3125in" id="Picture_x0020_3" src="cid:image003.png@01D6762B.BCF20FE0" alt="cid:image003.png@01D2789A.338CAE00"></span></a><span style="color:#5B9BD5"> </span><a href="https://www.youtube.com/channel/UCBa0vLyn1ZO7tW-RyJOrxPA"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="30" height="30" style="width:.3125in;height:.3125in" id="Picture_x0020_4" src="cid:image004.png@01D6762B.BCF20FE0" alt="cid:image004.png@01D2789A.338CAE00"></span></a><span style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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