<?php
//
// Copyright 2010, Julian Catchen <jcatchen@uoregon.edu>
//
// This file is part of Stacks.
//
// Stacks is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Stacks 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 General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
//

//
// Credentials to access Stacks MySQL databases
//
$db_user     = "dbuser";
$db_pass     = "dbpass";
$db_host     = "localhost";

//
// Path to the MySQL client program
//
$mysql_bin = "/usr/bin/mysql";

//
// File system location of PHP/HTML files
//
$system_path = "/Users/runner/bioconda/conda-bld/stacks_1593769799108/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/share/stacks/" . "php/";

//
// Location of perl script to run the exporting jobs.
//
$export_cmd  = "/Users/runner/bioconda/conda-bld/stacks_1593769799108/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/" . "stacks_export_notify.pl";

//
// Name to print in page header
//
$site_title  = "Stacks Analysis Pipeline";

//
// URL path to root of PHP/HTML files
//
$root_path   = "/stacks";
$img_path    = "/stacks/images";

//
// Length to wrap sequences at.
// 
$display_len = 80;

//
// Colors for printing alleles/haplotypes
//
$colors = array("#008000",
		"#c00000",
		"#ffc600",
		"#29356c",
		"#860000",
		"#dc6200",
		"#4b398e",
		"#008f56",
		"#bf1e25",
		"#4cb8ff");
$color_size = count($colors);

//
// Color map version 2; for printing alleles/haplotypes.
//
$color_map = array(
    'a' => "#0074D9", // Blue
    'b' => "#FF4136", // Red 
    'c' => "#008000", // Dark Green
    'd' => "#FF851B", // Orange 
    'e' => "#001f3f", // Navy
    'f' => "#85144b", // Maroon 
    'g' => "#F012BE", // Fuchsia 
    'h' => "#39CCCC", // Teal 
    'i' => "#3D9970", // Olive 
    'j' => "#01FF70", // Lime 
    'k' => "#FFDC00", // Yellow 
    'l' => "#B10DC9", // Purple 
    'm' => "#111111", // Black 
    'n' => "#7FDBFF", // Aqua 
    'o' => "#AAAAAA", // Gray 
    'p' => "#DDDDDD", // Silver 
    'q' => "#2ECC40", // Green 
    'r' => "#c00000",
    's' => "#ffc600",
    't' => "#29356c",
    'u' => "#860000",
    'v' => "#dc6200",
    'w' => "#4b398e",
    'x' => "#008f56",
    'y' => "#bf1e25",
    'z' => "#4cb8ff",
    'A' => "#26081C",
    'B' => "#C44900",
    'C' => "#036016",
    'D' => "#936426",
    'E' => "#E87EA1",
    'F' => "#692E38",
    'G' => "#19423F",
    'H' => "#625F64",
    'I' => "#432534",
    'J' => "#323845",
    'K' => "#758E4F",
    'L' => "#B287A3",
    'M' => "#C0F8D1",
    'N' => "#03440C",
    'O' => "#8EDCE6",
    'P' => "#D5DCF9",
    'Q' => "#A7B0CA",
    'R' => "#0CBABA",
    'S' => "#725E54",
    'T' => "#EE2677",
    'U' => "#84A98C",
    'V' => "#FCCA46",
    'W' => "#A1C181",
    'X' => "#443627",
    'Y' => "#FE7F2D",
    'Z' => "#2EBE62"
);
$color_map_size = count($color_map);

?>
