Configuration files

You can skip this section if you wish to install the GenIE-Sys using Graphical User Interface (GUI).

There are two configuration file associated with GenIE-Sys. One file for storing the database information (geniesys/plugins/settings.php) and other one (geniesys/plugins/config.json)for storing the sequence files and blast indices.

Here is the brief explanation to thegeniesys/plugins/settings.phpfile that we use with GenIE-Sys.

/*Define your base url with trailing slash*/
$GLOBALS["base_url"]='http://localhost:[port number]/geniesys/';
OR
$GLOBALS["base_url"]='http://localhost:[port number]';

Here is the example ofgeniesys/plugins/settings.phpfile that we use with GenIE-Sys.

global $db_species_array;
$db_species_array=array($db_name=>"species 1");
/*Here you can listed background colors correspond to each species. */
global $db_species_color_array;
$db_species_color_array=array("new_database"=>"#86c0a6");
/*You dont need to change anything here*/
$db_key_array=array_keys($db_species_array);
$db_values_array=array_values($db_species_array);
if(isset($_COOKIE['genie_select_species'])) {
$selected_database=$_COOKIE['genie_select_species'];
} else {
$selected_database=$db_key_array[0];
$_COOKIE['genie_select_species']=$db_key_array[0];
}
/*Please state the mysql username and password for above databases. It's important to grant only SELECT permissio to all the tables except defaultgenebaskets and genebasket tables*/
global $db_url;
$db_url= array ('genelist'=>'mysqli://geniecmsuser:[email protected]/'.$selected_database);
/*Define your base url with trailing slash*/
$GLOBALS["base_url"]='http://localhost:'.$_SERVER['SERVER_PORT'].'/geniesys/';
//Settings SQL modes here, allows for disabling the default STRICT_TRANS_TABLES which prevents PHP from inserting '' in auto_increment fields.
$db_settings['modes'] = "ONLY_FULL_GROUP_BY,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION";

Here is the brief explanation to thegeniesys/plugins/config.jsonfile that we use with GenIE-Sys.

"datasets":[
{
"number": 1,
"group_name": " Group name",
"dataset_path":"Path to the BLAST database",
"molecule_type":"This could be either nucleotide or protein",
"user_friendly_name":"Friendly username shows to the user"
}
]

Here is the example ofgeniesys/plugins/config.jsonfile that we use with GenIE-Sys.

"selection_box":[{"height":420,"width":400}],
"datasets":[
{
"number": 1,
"group_name": "Genomes",
"dataset_path":"data/blast/genome",
"molecule_type":"nucleotide",
"user_friendly_name":"Arabidopsis thaliana Genomes"
},{
"number": 2,
"group_name": "Transcripts",
"dataset_path":"data/blast/transcript",
"molecule_type":"nucleotide",
"user_friendly_name":"Arabidopsis thaliana Transcripts"
},{
"number": 3,
"group_name": "CDS",
"dataset_path":"/data/blast/cds",
"molecule_type":"nucleotide",
"user_friendly_name":"Arabidopsis thaliana CDS"
},{
"number": 4,
"group_name": "Protein",
"dataset_path":"data/blast/protein",
"molecule_type":"protein",
"user_friendly_name":"Arabidopsis thaliana protein"
}
],
"default_jbrowse_dataset_directory":"Fptr"
}