Skip to content
Perl PLpgSQL JavaScript Other TSQL C++ Other
Branch: devel
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
bin
ddl
lib
root
script
t
.gitignore
Changes
Licence
Makefile.PL
README
dist.ini
human_genes_79.yaml
mouse_genes_79.yaml
wge.conf
wge.psgi
wge_schema_2017_09_29.sql

README

    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"
You can’t perform that action at this time.