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EnzymeFunctionInitiative / efi-web

Replaces the est-web and gnt-web repositories by unifying them into a single repo.
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efi-web

Build Status

The web interface for the EFI Tools, https://github.com/EnzymeFunctionInitiative/EFITools

LINUX INSTALLATION

Ensure that the php-pdo, php-mysqlnd, php-mbstring PHP packages are installed.

bin/setup-composer.sh
php composer.phar install

Configure Apache for efi-web/html path

Open terminal.

cd efi-web
bin/setup-composer.sh
php composer.phar install

WEB SITE CONFIGURATION

DATABASE SETUP

Create database efi_web, using SQL in sql/01_COMPLETE_ALL_TOOLS.sql

After database is created, apply any other SQL files in sql

Create user efi_web and set a password

This can be done with phpMySqlAdmin control panel, or with the terminal:

For example:

mysqladmin -u root create efi_web
mysql -u root efi_web < sql/01_COMPLETE_ALL_TOOLS.sql
mysql -u root efi_web < sql/create_user.sql.example

MAKE SURE TO UPDATE THE PASSWORD IN sql/create_user.sql.example

CREATE UPLOAD DIRECTORIES

mkdir efi-est/uploads
chown www-data:www-data efi-est/uploads
mkdir efi-gnt/uploads
chown www-data:www-data efi-gnt/uploads
mkdir efi-cgfp/uploads
chown www-data:www-data efi-cgfp/uploads
mkdir efi-est/log
chown www-data:www-data efi-est/log
mkdir efi-gnt/log
chown www-data:www-data efi-gnt/log
mkdir efi-cgfp/log
chown www-data:www-data efi-cgfp/log

where www-data is the Apache user/group (set appropriately).

EFI-WEB CONFIGURATION FILES

cp conf/settings_base.inc.php.example conf/settings_base.inc.php
cp conf/settings_paths.inc.php.example conf/settings_paths.inc.php
cp conf/settings_auth.inc.php.example conf/settings_auth.inc.php
cp conf/settings.inc.php.example conf/settings.inc.php
cp conf/efi_est/settings.inc.php.example conf/efi_est/settings.inc.php
cp conf/efi_est/settings_shared.inc.php.example conf/efi_est/settings_shared.inc.php
cp conf/efi_gnt/settings.inc.php.example conf/efi_gnt/settings.inc.php
cp conf/efi_cgfp/settings.inc.php.example conf/efi_cgfp/settings.inc.php
cp conf/efi_cgfp/settings_shared.inc.php.example conf/efi_cgfp/settings_shared.inc.php
cp conf/users/settings.inc.php.example conf/users/settings.inc.php
cp conf/training/settings.inc.php.example conf/training/settings.inc.php
cp conf/training/settings_examples.inc.php.example conf/training/settings_examples.inc.php

When entering file or directory paths on Windows into the config files always use the forward slash for directory separator char (/).

Main Config

Change the following in conf/settings_base.inc.php:

__BASE_WEB_ROOT__ (on XAMPP set to http://localhost)
__TIMEZONE__
__ADMIN_EMAIL__
__ERROR_ADMIN_EMAIL__
__FEEDBACK_EMAIL__
__EST_RESULTS_DIR__
__BASE_WEB_PATH__ (optional, but if you are using EST on an Alias (like in XAMPP) then set to that Alias (e.g. /efi-web)
__MYSQL_HOST__ (left at default if using same paramters as in Database Setup)
__MYSQL_DATABASE__ (left at default if using same paramters as in Database Setup)
__MYSQL_USER__ (left at default if using same paramters as in Database Setup)
__MYSQL_PASSWORD__ (set to password in Database Setup)
__MYSQL_AUTH_DATABASE__ (left at default if using same paramters as in Database Setup)

For EST_RESULTS_DIR on Windows this can be left blank because there is no EFITools backend installation available.

To use sample data on Windows:

__EST_RESULTS_DIR__ = C:/efi/web_sample_data/est

EST

Change the following in conf/efi_est/settings.inc.php:

__LOG_FILE__
__UPLOADS_DIR__

GNT

Change the following in conf/efi_gnt/settings.inc.php:

__OUTPUT_DIR__
__DIAGRAM_OUTPUT_DIR__
__UPLOAD_DIR__
__LOG_FILE__

CGFP

Change

__OUTPUT_DIR__
__UPLOAD_DIR__
__LOG_FILE__
__METAGENOME_DB_LIST__

LOAD SAMPLE DATA

To use the sample data change __RETENTION_DAYS and FILE_RETENTION_DAYS__ to 1000. This should be set to the default of 30 on production systems.

Download web_sample_data and family_sizes from https://efi.igb.illinois.edu/databases/sample_data/ and unzip.

mysql -u root efi_web < web_sample_data/install_examples.sql
mysql -u root efi_web < load_family_sizes.sql

MAKE SYMLINKS

On Linux, symlink the following:

ln -s __EST_RESULTS_DIR__ html/efi-est/results
ln -s (GNT)__OUTPUT_DIR__ html/efi-gnt/results
ln -s (GNT)__DIAGRAM_OUTPUT_DIR__ html/efi-gnt/gnd_results
ln -s (ShortBred)__OUTPUT_DIR__ html/efi-cgfp/results

Adjust paths accordingly.