WGE Wellcome Sanger Institute Genome Editor
Copyright (C) 2019 Genome Research Limited
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
To use this app first create an empty postgres database, then:
log in to your db:
psql --host <host> --port <port> --user <username> <dbname>
load the sql:
begin;
\i ~/WGE/ddl/2/wge_tables_new.sql
commit;
Add the database connection information to the config file specified by the WGE_DBCONNECT_CONFIG environment variable:
WGE:
schema_class: WGE::Model::Schema
dsn: mydsn
AutoCommit: 1
user: my
password: mypass
Set the WGE_DB environment variable to the name of the connection profile to use (e.g., "WGE" to use the above)
Bring up the webapp to make sure everything is working:
script/wge_server.pl --port 3030
Now the webapp can see your db lets load some data. Note: Make sure ensembl is installed and in your PERL5LIB.
We have included all the genes and exons (for mouse & human) from ensembl build 73, so load them:
perl -I lib ./bin/load_genes.pl human_genes_73.yaml
Or if you want to generate the yaml file:
perl ./bin/get_all_genes.pl <species>
To add all the crispr pairs to the db:
perl -I lib ./bin/get_all_genes.pl
If you make any changes to the db you can regenerate the DBIx::Class models with:
perl ./bin/dump_schema.pl
Create a separate test database before running tests.
Test::WGE::load_fixtures will delete all database content!
When you "use Test::WGE" the database connection profile named "WGE_TEST" will be used.
To override this with your own test database set the WGE_TEST_DB environment variable to e.g., "MY_WGE_TEST"