WGE catalyst app http://www.sanger.ac.uk/htgt/wge/
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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"