A tool for annotation of next generation sequencing data with allele frequencies of populations from India.
#How to set up on RedHat: ##Perl Version -- Current Implementation At URMC Before anything happens, make sure you have the latest version of Perl.
- Now, install Catalyst, the Perl MVC from which the website is hosted. To quote the installation instructions from BrainBase:
I'm really sorry about this. Perl Catalyst is fantastic and amazing. But installation can sometimes be a route to no happiness. The most certain way to have a bad time installing Perl Catalyst is to try to install it on an old Linux system. By "old" I mean anything that is not running the most up-to-date kernel. I have the best experience installing Perl Catalyst right on top of a fresh Linux install.
perl -MCPAN -e 'install Catalyst::Runtime'
perl -MCPAN -e 'install Catalyst::Devel'
- You will need the following Catalyst Plugins from CPAN: Catalyst::Plugin::Authentication Catalyst::Authentication::Realm::SimpleDB Catalyst::Plugin::Session Catalyst::Plugin::Session::Store::File Catalyst::Plugin::Session::State::Cookie Catalyst::Helper::Model::DBIC::Schema Catalyst::Controller::FormBuilder Catalyst::View::TT MooseX::MarkAsMethods MooseX::NonMoose DBIx::Class::Schema::Loader DBIx::Class::TimeStamp DBIx::Class::PassphraseColumn HTML::FormHandler::Model::DBIC There is a way to get MCPAN to auto install all these modules without the prompt asking you for yes / no inputs.
To do this, simply bring up a CPAN shell:
perl -MCPAN -e shell
Run these two commands in the CPAN shell:
o conf prerequisites_policy follow
o conf commit
Now, exit the CPAN shell, start the CPAN shell, and try to install a module that you need. All dependencies will be automatically confirmed, downloaded and installed. (from https://major.io/2009/01/01/cpan-automatically-install-dependencies-without-confirmation/) 3. put this code into a directory from where you normally host websites. 4. Configure MySQL / MariaDB for your Linux System. For Slackware 14.1 I follow the directions here: http://docs.slackware.com/howtos:databases:install_mysql_on_slackware If you follow the directions closely you should have no problem. 6. Once MySQL is configured log in as root: $ mysql -u root -p .. MariaDB> Check that InnoDB is supported. MariaDB> SHOW VARIABLES LIKE 'have_innodb'; If mysql returns the value as YES it is supported. 7. Create a database called IndiaAlleleFinderDB
MariaDB> CREATE DATABASE IndiaAlleleFinderDB;
MariaDB> GRANT ALL PRIVILEGES ON IndiaAlleleFinderDB.* TO [username] IDENTIFIED BY '[PASSWORD]';
MariaDB> FLUSH PRIVILEGES;
MariaDB> exit
Bye
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Configure mysql:
mysql --u root --p IndiaAlleleFinderDB < mysql-dump.sql
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Generate your Catalyst model (maybe optional):
$ script/brainbase_create.pl model DB DBIC::Schema IndiaAlleleFinderDB::Schema create=static \ components=TimeStamp,PassphraseColumn dbi:mysql:indiaallelefinderdb '[username]' '[password]' '{ AutoCommit => 1 }'
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Open terminal and go to the /IndiaAlleleFinder folder & start the server:
$ script/indiaallelefinder_server.pl -rp 3000
Or whatever port you might wish to run it on.
##Python Version (In Progress) First, Install pip:
- Follow these instructions: https://pip.pypa.io/en/latest/installing/ Download the following: https://bootstrap.pypa.io/get-pip.py and run python get-pip.py
Next, Install Flask and and its Associated Packages
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Now, pip install flask. http://flask.pocoo.org/docs/0.10/installation/#installation *Make sure you have mysql56-server or its equivalent installed. for example on a mac this would be: sudo port install mysql56-server
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sudo pip install MySQL-python
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sudo pip install flask-mysqldb
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sudo pip install flask-SQLAlchemy Go to the directory where you've downloaded India Allele Finder, and Run It:
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python main.py &
###Flask MySQL Database Configuration
mysql --u root --p IndiaAlleleFinderDB < mysql-dump.sql
then edit the corresponding line in main.py: app.config['SQLALCHEMY_DATABASE_URI'] = 'mysql://root:root@localhost/indiaAlleleFinderDB'
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