Mercurial > repos > melissacline > xena_import

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            <title>Galaxy Tool Shed</title>
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            right: 0 !important;
    }
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    <style type="text/css">
        body { margin: 0; padding: 0; overflow: hidden; }
        #left {
            background: #C1C9E5 url(/static/style/menu_bg.png) top repeat-x;
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        .unified-panel-body {
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        .toolMenu {
            margin-left: 10px;
        }
    </style>


    <script src="/static/scripts/libs/jquery/jquery.js?v=1409176523" type="text/javascript"></script>
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    <script src="/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1409176523" type="text/javascript"></script>

    <script src="/static/scripts/mvc/ui.js?v=1409176523" type="text/javascript"></script>

    <script type="text/javascript">
        var galaxy_config = {
            url: {
                styles : "/static/style"
            }
        };

        if (window != window.top)
            $('<link href="' + galaxy_config.url.styles + '/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');

        // console protection
        window.console = window.console || {
            log     : function(){},
            debug   : function(){},
            info    : function(){},
            warn    : function(){},
            error   : function(){},
            assert  : function(){}
        };

        // Set up needed paths.
        var galaxy_paths = new GalaxyPaths({
            root_path: '/',
            image_path: '/static/images',

            tool_url: '/api/tools',
            history_url: '/api/histories',

            datasets_url: '/api/datasets',
            sweepster_url: '/visualization/sweepster',
            visualization_url: '/visualization/save',
        });

        require.config({
            baseUrl: "/static/scripts",
            shim: {
                "libs/underscore": { exports: "_" },
                "libs/backbone/backbone": { exports: "Backbone" },
                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
            }
        });

        var frame_manager = null;
        require(['galaxy.frame'], function(frame) { this.frame_manager = new frame.GalaxyFrameManager(galaxy_config); });
    </script>


    </head>

    <body scroll="no" class="full-content ">
        <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;">
            <div id="background"></div>
            <div id="masthead" class="navbar navbar-fixed-top">
                <div class="masthead-inner navbar-inner">


    <div style="position: relative; right: -50%; float: left;">
        <div style="display: block; position: relative; right: 50%;">

            <ul class="nav" border="0" cellspacing="0">


                    <li class="" style="">
                            <a class="" data-toggle="dropdown" target="_parent" href="/repository">Repositories</a>
                    </li>


                    <li class=" admin-only" style="display: none;">
                            <a class="" data-toggle="dropdown" target="_parent" href="/admin">Admin</a>
                    </li>


                    <li class=" dropdown" style="">
                            <a class=" dropdown-toggle" data-toggle="dropdown">Help<b class='caret'></b></a>
                            <ul class="dropdown-menu">
                                        <li>

                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/Support">Support</a>
                                        </li>
                                        <li>

                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/Tool%20Shed">Tool shed wiki</a>
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                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/">Galaxy wiki</a>
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                                        <li>

                                            <a target="_blank" href="http://galaxycast.org">Video tutorials (screencasts)</a>
                                        </li>
                                        <li>

                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/Citing%20Galaxy">How to Cite Galaxy</a>
                                        </li>
                            </ul>
                    </li>


                    <li class=" dropdown" style="">
                            <a class=" dropdown-toggle" data-toggle="dropdown">User<b class='caret'></b></a>
                            <ul class="dropdown-menu">
                                        <li>

                                            <a target="galaxy_main" href="/user/login">Login</a>
                                        </li>
                                        <li>

                                            <a target="galaxy_main" href="/user/create?cntrller=user">Register</a>
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                            </ul>
                    </li>


                    <li class=" dropdown" style="display: none;">
                            <a class=" dropdown-toggle" data-toggle="dropdown">User<b class='caret'></b></a>
                            <ul class="dropdown-menu">
                                        <li>
                                            <a>Logged in as <span id="user-email"></span></a>
                                        </li>
                                        <li>

                                            <a target="galaxy_main" href="/user?cntrller=user">Preferences</a>
                                        </li>
                                        <li>

                                            <a target="galaxy_main" href="/user/api_keys?cntrller=user">API Keys</a>
                                        </li>
                                        <li>

                                            <a target="_top" href="/user/logout">Logout</a>
                                        </li>
                                        <li class="divider"></li>
                            </ul>
                    </li>

            </ul>
        </div>
    </div>

    <div class="title">
        Galaxy Tool Shed
        </a>
    </div>

                </div>
            </div>
            <div id="messagebox" class="panel-info-message">
            </div>


    <div id="overlay" style='display: none;'>

        <div id="overlay-background" class="modal-backdrop fade "></div>

        <div id="dialog-box" class="modal dialog-box" border="0" style='display: none;'>
                <div class="modal-header">
                    <span><h3 class='title'></h3></span>
                </div>
                <div class="modal-body"></div>
                <div class="modal-footer">
                    <div class="buttons" style="float: right;"></div>
                    <div class="extra_buttons" style=""></div>
                    <div style="clear: both;"></div>
                </div>
        </div>

    </div>

                <div id="left">


    <div class="unified-panel-header" unselectable="on">
        <div class='unified-panel-header-inner'>29 valid tools on Aug 27, 2014</div>
    </div>
    <div class="unified-panel-body">
        <div class="toolMenu">
            <div class="toolSectionList">
                    <div class="toolSectionPad"></div>
                    <div class="toolSectionTitle">
                        All Repositories
                    </div>
                    <div class="toolTitle">
                        <a href="/repository">Browse by category</a>
                    </div>
            </div>
        </div>
    </div>

                    <div class="unified-panel-footer">
                        <div class="panel-collapse"></span></div>
                        <div class="drag"></div>
                    </div>
                </div>
            <div id="center">


    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="/repository/view_repository?status=done&message=&id=149c5ffa3420467d"></iframe>

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    <script src="/static/scripts/libs/jquery/jquery.event.drag.js?v=1409176523" type="text/javascript"></script>
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<script src="/static/scripts/libs/jquery/jquery.rating.js?v=1409176523" type="text/javascript"></script>
<script src="/static/scripts/galaxy.panels.js?v=1409176523" type="text/javascript"></script>
    <script type="text/javascript">

    ensure_dd_helper();

            var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .panel-collapse" ) } );
            force_left_panel = function( x ) { lp.force_panel( x ) };


    </script>
    <![if !IE]>
    <script type="text/javascript">
        var upload_form_error = function( msg ) {
            if ( ! $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").size() ) {
                $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage" name="upload_error">' + msg + '</div><p/>' );
            } else {
                $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").text( msg );
            }
        }
        var uploads_in_progress = 0;
        jQuery( function() {
            $("iframe#galaxy_main").load( function() {
                $(this).contents().find("form").each( function() {
                    if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){
                        $(this).submit( function() {
                            // Only bother using a hidden iframe if there's a file (e.g. big data) upload
                            var file_upload = false;
                            $(this).find("input[galaxy-ajax-upload]").each( function() {
                                if ( $(this).val() != '' ) {
                                    file_upload = true;
                                }
                            });
                            if ( ! file_upload ) {
                                return true;
                            }
                            // Make a synchronous request to create the datasets first
                            var async_datasets;
                            var upload_error = false;
                            $.ajax( {
                                async:      false,
                                type:       "POST",
                                url:        "/tool_runner/upload_async_create",
                                data:       $(this).formSerialize(),
                                dataType:   "json",
                                success:    function(array_obj, status) {
                                                if (array_obj.length > 0) {
                                                    if (array_obj[0] == 'error') {
                                                        upload_error = true;
                                                        upload_form_error(array_obj[1]);
                                                    } else {
                                                        async_datasets = array_obj.join();
                                                    }
                                                } else {
                                                    // ( gvk 1/22/10 ) FIXME: this block is never entered, so there may be a bug somewhere
                                                    // I've done some debugging like checking to see if array_obj is undefined, but have not
                                                    // tracked down the behavior that will result in this block being entered.  I believe the
                                                    // intent was to have this block entered if the upload button is clicked on the upload
                                                    // form but no file was selected.
                                                    upload_error = true;
                                                    upload_form_error( 'No data was entered in the upload form.  You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch data.' );
                                                }
                                            }
                            } );
                            if (upload_error == true) {
                                return false;
                            } else {
                                $(this).find("input[name=async_datasets]").val( async_datasets );
                                $(this).append("<input type='hidden' name='ajax_upload' value='true'>");
                            }
                            // iframe submit is required for nginx (otherwise the encoding is wrong)
                            $(this).ajaxSubmit( { iframe:   true,
                                                  complete: function (xhr, stat) {
                                                                uploads_in_progress--;
                                                                if (uploads_in_progress == 0) {
                                                                    window.onbeforeunload = null;
                                                                }
                                                            }
                                                 } );
                            uploads_in_progress++;
                            window.onbeforeunload = function() { return "Navigating away from the Galaxy analysis interface will interrupt the file upload(s) currently in progress.  Do you really want to do this?"; }
                            if ( $(this).find("input[name='folder_id']").val() != undefined ) {
                                var library_id = $(this).find("input[name='library_id']").val();
                                var show_deleted = $(this).find("input[name='show_deleted']").val();
                                if ( location.pathname.indexOf( 'admin' ) != -1 ) {
                                    $("iframe#galaxy_main").attr("src","/library_common/browse_library?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
                                } else {
                                    $("iframe#galaxy_main").attr("src","/library_common/browse_library?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
                                }
                            } else {
                                $("iframe#galaxy_main").attr("src","/tool_runner/upload_async_message");
                            }
                            return false;
                        });
                    }
                });
            });
        });
    </script>
    <![endif]>

</html>
author	melissacline
date	Wed, 03 Sep 2014 15:29:10 -0400
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