Step 1.3: git clone ensembl repositories
Reusing this script
The
update-ensembl-code.sh
script should be run again (as Step 3.1) following data import in Stage 2/Stage 3. To set up a mirror site, continue directly to Step 3.1: Update Ensembl webcode for full details of additional configuration options.
Running the update-ensembl-code.sh
script will git clone
/git pull
a set of (mostly Ensembl) repositories required for Core/Compara Import and for hosting an Ensembl instance.
cd ~/ei/em
./update-ensembl-code.sh ../conf/setup.ini
Testing your setup
With the basic setup complete, you can now jump directly to Step 3.2: Reload Ensembl website to launch a local Ensembl instance.
Configuration options
Two stanzas in setup.ini
are relevant at this stage:
[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, theDB_FALLBACK_HOST
host will be queried to find any required databases that are not available onDB_HOST
-
DB_FALLBACK2_HOST
etc. - especially with EnsemblGenomes sites, remote databases may be found on more than one host, theDB_FALLBACK2_HOST
host will be queried to find any required databases that are not available onDB_HOST
orDB_FALLBACK_HOST
[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
andBIOPERL_URL
/BIOPERL_BRANCH
are always required. Several Ensel]mbl repositories aregit clone
d fromENSEMBL_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 toensembl-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 Ensemblpublic-plugins
repository by specifying the directory and package name of each repository as inPUBLIC_PLUGINS = [ ensembl|EnsEMBL::Ensembl genoverse|EnsEMBL::Genoverse ]
The remaining section in setup.ini
, [DATA_SOURCE], can also be edited at this stage - see Step 4.1: Update Ensembl webcode for details.
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