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Step 3.1: Update Ensembl webcode

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To resume Ensembl web setup following Stage 2/3, edit setup.ini to add operophtera_brumata_v1_core_31_84_1 to [DATA_SOURCE] SPECIES_DBS

Running this script now will restore all ensembl repositories and update configuration files for the Ensembl website.

cd ~/ei/em
./update-ensembl-code.sh ../conf/setup.ini

Configuration options

[DATABASE]
    DB_HOST = localhost
    DB_PORT = 3306
    DB_USER = anonymous
    DB_PASS =

    DB_SESSION_HOST = localhost
    DB_SESSION_PORT = 3306
    DB_SESSION_USER = ensrw
    DB_SESSION_PASS = ensrw

    DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.uk
    DB_FALLBACK_PORT = 4157
    DB_FALLBACK_USER = anonymous
    DB_FALLBACK_PASS =

    DB_FALLBACK2_HOST = ensembldb.ensembl.org
    DB_FALLBACK2_PORT = 3306
    DB_FALLBACK2_USER = anonymous
    DB_FALLBACK2_PASS =

Four subsections with DB_[*_]HOST, DB_[*_]PORT, DB_[*_]USER and DB_[*_]PASS variables specify connection settings for:

  • DB_HOST etc. - the primary database host with species/multi-species databases.

  • DB_SESSION_HOST etc. - user-specific information, typically the only database to require read-write access and therefore a password protected connection.

  • DB_FALLBACK_HOST etc. - to reduce the amount of locally hosted data, it is often desirable to use alternate sources for some databases, the DB_FALLBACK_HOST host will be queried to find any required databases that are not available on DB_HOST

  • DB_FALLBACK2_HOST etc. - especially with EnsemblGenomes sites, remote databases may be found on more than one host, the DB_FALLBACK2_HOST host will be queried to find any required databases that are not available on DB_HOST or DB_FALLBACK_HOST

  • [REPOSITORIES]

[REPOSITORIES]
    ENSEMBL_URL = https://github.com/Ensembl
    ENSEMBL_BRANCH = release/84

    BIOPERL_URL = https://github.com/bioperl
    BIOPERL_BRANCH = master

    EG_METAZOA_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-metazoa
    EG_METAZOA_PLUGIN_BRANCH = release/eg/31
    EG_METAZOA_PLUGIN_PACKAGE = EG::Metazoa

    API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
    API_PLUGIN_BRANCH = release/eg/31
    API_PLUGIN_PACKAGE = EG::API

    EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
    EG_COMMON_PLUGIN_BRANCH = release/eg/31
    EG_COMMON_PLUGIN_PACKAGE = EG::Common

    PUBLIC_PLUGINS = [ ]

Connection/branch information for the Github repositories to be cloned

  • ENSEMBL_URL/ENSEMBL_BRANCH and BIOPERL_URL/BIOPERL_BRANCH are always required. Several Ensel]mbl repositories are git cloned from ENSEMBL_URL for both the Ensembl website and to support the import pipeline.

  • Additional plugins can be loaded from any public git repository by specifying <NAME>_PLUGIN_URL, <NAME>_PLUGIN_BRANCH and <NAME>_PLUGIN_PACKAGE as above. Plugins specified in this way will be added to ensembl-webcode/conf/Plugins.pm in the order they are listed in the .ini file so those at the top of the list will overwrite functions in plugins further down the list.

  • PUBLIC_PLUGINS can be loaded from the Ensembl public-plugins repository by specifying the directory and package name of each repository as in PUBLIC_PLUGINS = [ ensembl|EnsEMBL::Ensembl genoverse|EnsEMBL::Genoverse ]

  • [DATA_SOURCE] 

[DATA_SOURCE]
  SPECIES_DBS = [ bombyx_mori_core_31_84_1 danaus_plexippus_core_31_84_1 heliconius_melpomene_core_31_84_1 melitaea_cinxia_core_31_84_1 operophtera_brumata_core_31_84_1 ]
  MULTI_DBS = [ ensemblgenomes_ontology_31_84 ensembl_compara_pan_homology_31_84 ensemblgenomes_info_31 ensembl_compara_metazoa_31_84  ensembl_archive_84 ensembl_website_84 ]
  • SPECIES_DBS a space separated list of ensembl core dbs in square braces
  • SPECIES_DB_AUTO_EXPAND to save listing all dbs for a given species this variable may be used to specify a set of replacement strings to attempt to connect to (e.g. specify SPECIES_DBS = [ homo_sapiens_core_83_38 ] and SPECIES_DB_AUTO_EXPAND = [ variation ] to also load the database homo_sapiens_variation_83_38, if it exists on [DATABASE] DB_HOST or DB_FALLBACK_HOST
  • MULTI_DBS - a space separated list of multispecies databases in square braces

Updated less than a minute ago