[ensembl-dev] Ensembl Rest Follow up

Sage Hornung sage.hornung at neogenomics.com
Wed Aug 19 22:03:20 BST 2020


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.
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)
I want to point the REST instance  I am currently  setting  up to our instance of the CRCh37 database once its ready.

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.
This would mean calling the database instead of using the cache files.
It would be great if I could make a couple small calls to the ensemble DB using the rest interface

It seems as if I can add any configurations to ensembl_rest.conf found here  https://uswest.ensembl.org/info/docs/tools/vep/script/vep_options.html  to the section of the <Controller::VEP> and they should be passed  to vep

There is also a section at the top of the ensembl_rest.conf

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

  ###### Database settings. Use if you want to connect to a single database instance. Common options are given below
  host = ensembldb.ensembl.org
  port = 3337
  user = anonymous

  version = 100
  verbose = 1

  fasta             = Homo_sapiens.GRCh37.75.dna.toplevel.fa # path to Human toplevel fasta file
# Default parameters for running vep
  cache_region_size = 1000000
  chunk_size        = 50000
  whole_genome      = 1
  compress          = gzip -dc
  terms             = SO
  cache             = 0
  #merged            = 0
  failed            = 0
  core_type         = core
  quiet             = 1
  sift              = b
  polyphen          = b
  symbol            = 1
  regulatory        = 1
  biotype           = 1
  rest              = 1
  check_existing    = 1 # adds some performance penalty, mitigated by tabix-converting the cache (http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#convert)
  fork              = 3
  max_post_size     = 1000
  warning_file      = STDERR # controls VEP logging, not Catalyst
  plugin_config     = # path to plugin config
  dir_plugins       = # path to VEP_plugins checkout
  #dir               = /home/ensembl/.vep/homo_sapiens/100_GRCh37
  database = 1
  #host              = ensembldb.ensembl.org
  #port              = 3337
  #assebbly          = GRCh37
  #user              = anonymous

I still get this error

The VEP can read gene data from either a local cache or local/remote databases.

Using a cache is the fastest and most efficient way to use the VEP. The
included INSTALL.pl script can be used to fetch and set up cache files from the
Ensembl FTP server. Simply run "perl INSTALL.pl" and follow the instructions, or
see the documentation pages listed below.

If you have already set up a cache, use "--cache" or "--offline" to use it.

It is possible to use the public databases hosted at ensembldb.ensembl.org, but
this is slower than using the cache and concurrent and/or long running VEP jobs
can put strain on the Ensembl servers, limiting availability to other users.

To enable using databases, add the flag "--database".

Installer: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer
Cache: http://www.ensembl.org/info/docs/tools/vep/script/index.html#cache

     at /home/ensembl/ensembl-api-folder/ensembl-vep/modules/Bio/EnsEMBL/VEP/Config.pm line 686.

2020/08/19 13:40:22 (6) Serialize.pm 51> Serializing with Catalyst::Action::Serialize::JSON::XS
2020/08/19 13:40:22 (1) Catalyst.pm 2726> Response Code: 400; Content-Type: application/json; Content-Length: unknown

Thank you for the assistance

Sage Hornung
Software Engineer
NeoGenomics Laboratories, Inc.
2131 Faraday Avenue, Carlsbad, CA 92008
Phone: 760.516.5114
Cell: 760.755.3930
sage.hornung at neogenomics.com<mailto:sage.hornung at neogenomics.com>
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