Mercurial > repos > rabab > blast

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/display?to_ext=fasta	Mon Oct 29 17:16:18 2012 -0400
@@ -0,0 +1,565 @@
+<!DOCTYPE HTML>
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+<html>
+
+
+    <script type="text/javascript">
+        if ( window != top ) {
+            top.location.href = location.href;
+        }
+    </script>
+
+    <head>
+        <title>Galaxy</title>
+        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+        <meta name = "viewport" content = "maximum-scale=1.0">
+        <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">
+
+    <link href="/galaxy/static/style/base.css?v=1351538302" media="screen" rel="Stylesheet" type="text/css" />
+<link href="/galaxy/static/style/panel_layout.css?v=1351538302" media="screen" rel="Stylesheet" type="text/css" />
+<link href="/galaxy/static/style/jquery.rating.css?v=1351538302" media="screen" rel="Stylesheet" type="text/css" />
+    <style type="text/css">
+    body, html {
+        overflow: hidden;
+        margin: 0;
+        padding: 0;
+        width: 100%;
+        height: 100%;
+    }
+    #center {
+    }
+    </style>
+
+
+
+    <!--[if lt IE 7]>
+    <script src="/galaxy/static/scripts/libs/IE/IE7.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/IE/ie7-recalc.js?v=1351538302" type="text/javascript"></script>
+    <![endif]-->
+    <script src="/galaxy/static/scripts/libs/jquery/jquery.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/json2.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/bootstrap.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/underscore.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/backbone/backbone.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/backbone/backbone-relational.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/handlebars.runtime.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/mvc/ui.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/galaxy.base.js?v=1351538302" type="text/javascript"></script>
+    <script type="text/javascript">
+        // Set up needed paths.
+        var galaxy_paths = new GalaxyPaths({
+            root_path: '/galaxy/',
+            image_path: '/galaxy/static/images',
+
+            tool_url: '/galaxy/api/tools',
+            history_url: '/galaxy/api/histories',
+
+            datasets_url: '/galaxy/api/datasets',
+            sweepster_url: '/galaxy/visualization/sweepster',
+            visualization_url: '/galaxy/visualization/save',
+        });
+    </script>
+
+
+    </head>
+
+    <body scroll="no" class="">
+            <noscript>
+                <div class="overlay overlay-background">
+                    <div class="modal dialog-box" border="0">
+                        <div class="modal-header"><h3 class="title">Javascript Required</h3></div>
+                        <div class="modal-body">The Galaxy analysis interface requires a browser with Javascript enabled. <br> Please enable Javascript and refresh this page</div>
+                    </div>
+                </div>
+            </noscript>
+        <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;">
+            <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=" active" style="">
+                <a class="" data-toggle="dropdown" target="_parent" href="/galaxy/root">Analyze Data</a>
+        </li>
+
+
+
+
+
+        <li class="" style="">
+                <a class="" data-toggle="dropdown" target="_parent" href="/galaxy/workflow">Workflow</a>
+        </li>
+
+
+
+
+
+        <li class=" dropdown" style="">
+                <a class=" dropdown-toggle" data-toggle="dropdown" target="_parent" href="/galaxy/library">Shared Data<b class='caret'></b></a>
+                <ul class="dropdown-menu">
+                            <li>
+
+                                <a href="/galaxy/library">Data Libraries</a>
+                            </li>
+                            <li class="divider"></li>
+                            <li>
+
+                                <a href="/galaxy/history/list_published">Published Histories</a>
+                            </li>
+                            <li>
+
+                                <a href="/galaxy/workflow/list_published">Published Workflows</a>
+                            </li>
+                            <li>
+
+                                <a href="/galaxy/visualization/list_published">Published Visualizations</a>
+                            </li>
+                            <li>
+
+                                <a href="/galaxy/page/list_published">Published Pages</a>
+                            </li>
+                </ul>
+        </li>
+
+
+
+
+
+        <li class=" dropdown" style="display: none;">
+                <a class=" dropdown-toggle" data-toggle="dropdown">Lab<b class='caret'></b></a>
+                <ul class="dropdown-menu">
+                            <li>
+
+                                <a href="/galaxy/requests">Sequencing Requests</a>
+                            </li>
+                            <li>
+
+                                <a href="/galaxy/requests/find_samples_index">Find Samples</a>
+                            </li>
+                            <li>
+
+                                <a target="galaxy_main" href="http://main.g2.bx.psu.edu/u/rkchak/p/sts">Help</a>
+                            </li>
+                </ul>
+        </li>
+
+
+
+
+
+        <li class=" dropdown" style="">
+                <a class=" dropdown-toggle" data-toggle="dropdown" target="_parent" href="/galaxy/visualization/list">Visualization<b class='caret'></b></a>
+                <ul class="dropdown-menu">
+                            <li>
+
+                                <a href="/galaxy/visualization/trackster">New Visualization</a>
+                            </li>
+                            <li>
+
+                                <a href="/galaxy/visualization/list">Saved Visualizations</a>
+                            </li>
+                </ul>
+        </li>
+
+
+
+
+
+
+        <li class=" admin-only" style="display: none;">
+                <a class="" data-toggle="dropdown" target="_parent" href="/galaxy/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="galaxy_main" href="http://slyfox.bx.psu.edu:8080/">Galaxy Q&A</a>
+                            </li>
+                            <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/">Galaxy Wiki</a>
+                            </li>
+                            <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="/galaxy/user/login">Login</a>
+                            </li>
+                            <li>
+
+                                <a target="galaxy_main" href="/galaxy/user/create?cntrller=user">Register</a>
+                            </li>
+                </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="/galaxy/user?cntrller=user">Preferences</a>
+                            </li>
+                            <li>
+
+                                <a target="galaxy_main" href="/galaxy/user/dbkeys">Custom Builds</a>
+                            </li>
+                            <li>
+
+                                <a target="_top" href="/galaxy/root?m_c=user&m_a=logout">Logout</a>
+                            </li>
+                            <li class="divider"></li>
+                            <li>
+
+                                <a target="galaxy_main" href="/galaxy/history/list">Saved Histories</a>
+                            </li>
+                            <li>
+
+                                <a target="galaxy_main" href="/galaxy/dataset/list">Saved Datasets</a>
+                            </li>
+                            <li>
+
+                                <a target="_top" href="/galaxy/page/list">Saved Pages</a>
+                            </li>
+                            <li>
+
+                                <a target="galaxy_main" href="/galaxy/user/api_keys?cntrller=user">API Keys</a>
+                            </li>
+                </ul>
+        </li>
+
+
+    </ul>
+
+    </div>
+    </div>
+
+    <div class="title">
+        <a href="/galaxy/">
+        <img border="0" src="/galaxy/static/images/galaxyIcon_noText.png">
+        Galaxy
+            <span>/ WUR</span>
+        </a>
+    </div>
+
+
+
+    <div class="quota-meter-container">
+        <div id="quota-meter" class="quota-meter">
+            <div id="quota-meter-bar" class="quota-meter-bar" style="width: 0px;"></div>
+                <div id="quota-meter-text" class="quota-meter-text">Using 0 bytes</div>
+        </div>
+    </div>
+
+
+                </div>
+            </div>
+            <div id="messagebox" class="panel--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'>
+            Tools
+        </div>
+    </div>
+    <div class="unified-panel-body" style="overflow: hidden;">
+        <iframe name="galaxy_tools" id="galaxy_tools" src="/galaxy/root/tool_menu" frameborder="0" style="position: absolute; margin: 0; border: 0 none; height: 100%; width: 100%;"> </iframe>
+    </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="/galaxy/user/login"></iframe>
+
+
+            </div>
+                <div id="right">
+
+    <div class="unified-panel-header" unselectable="on">
+        <div class="unified-panel-header-inner">
+            <div style="float: right">
+                <a id="history-options-button" class='panel-header-button' href="/galaxy/root/history_options" target="galaxy_main"><span class="ficon large cog"></span></a>
+            </div>
+            <div class="panel-header-text">History</div>
+        </div>
+    </div>
+    <div class="unified-panel-body" style="overflow: hidden;">
+        <iframe name="galaxy_history" width="100%" height="100%" frameborder="0" style="position: absolute; margin: 0; border: 0 none; height: 100%;" src="/galaxy/history"></iframe>
+    </div>
+
+                    <div class="unified-panel-footer">
+                        <div class="panel-collapse right"></span></div>
+                        <div class="drag"></div>
+                    </div>
+                </div>
+        </div>
+    </body>
+
+
+    <script src="/galaxy/static/scripts/libs/jquery/jquery.event.drag.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/jquery/jquery.event.hover.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/jquery/jquery.form.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/libs/jquery/jquery.rating.js?v=1351538302" type="text/javascript"></script>
+<script src="/galaxy/static/scripts/galaxy.panels.js?v=1351538302" 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 ) };
+
+            var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .panel-collapse" ), right: true } );
+            window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) };
+            force_right_panel = function( x ) { rp.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:        "/galaxy/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","/galaxy/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","/galaxy/library_common/browse_library?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
+                                }
+                            } else {
+                                $("iframe#galaxy_main").attr("src","/galaxy/tool_runner/upload_async_message");
+                            }
+                            return false;
+                        });
+                    }
+                });
+            });
+        });
+    </script>
+    <![endif]>
+
+    <script type="text/javascript">
+    // Set up GalaxyAsync object.
+    var galaxy_async = new GalaxyAsync();
+    galaxy_async.set_func_url(galaxy_async.set_user_pref, "/galaxy/user/set_user_pref_async");
+
+    $(function(){
+        // Init history options.
+        $("#history-options-button").css( "position", "relative" );
+        make_popupmenu( $("#history-options-button"), {
+            "History Lists": null,
+            "Saved Histories": function() {
+                galaxy_main.location = "/galaxy/history/list";
+            },
+            "Histories Shared with Me": function() {
+                galaxy_main.location = "/galaxy/history/list_shared";
+            },
+            "Current History": null,
+            "Create New": function() {
+                galaxy_history.location = "/galaxy/root/history_new";
+            },
+            "Clone": function() {
+                galaxy_main.location = "/galaxy/history/clone";
+            },
+            "Copy Datasets": function() {
+                galaxy_main.location = "/galaxy/dataset/copy_datasets";
+            },
+            "Share or Publish": function() {
+                galaxy_main.location = "/galaxy/history/sharing";
+            },
+            "Extract Workflow": function() {
+                galaxy_main.location = "/galaxy/workflow/build_from_current_history";
+            },
+            "Dataset Security": function() {
+                galaxy_main.location = "/galaxy/root/history_set_default_permissions";
+            },
+            "Show Deleted Datasets": function() {
+                galaxy_history.location = "/galaxy/history?show_deleted=True";
+            },
+            "Show Hidden Datasets": function() {
+                galaxy_history.location = "/galaxy/history?show_hidden=True";
+            },
+            "Purge Deleted Datasets": function() {
+                if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) {
+                    galaxy_main.location = "/galaxy/history/purge_deleted_datasets";
+                }
+            },
+            "Show Structure": function() {
+                galaxy_main.location = "/galaxy/history/display_structured";
+            },
+            "Export to File": function() {
+                galaxy_main.location = "/galaxy/history/export_archive";
+            },
+            "Delete": function() {
+                if ( confirm( "Really delete the current history?" ) ) {
+                    galaxy_main.location = "/galaxy/history/delete_current";
+                }
+            },
+            "Delete Permanently": function() {
+                if ( confirm( "Really delete the current history permanently? This cannot be undone." ) ) {
+                    galaxy_main.location = "/galaxy/history/delete_current?purge=True";
+                }
+            },
+            "Other Actions": null,
+            "Import from File": function() {
+                galaxy_main.location = "/galaxy/history/import_archive";
+            }
+        });
+
+    });
+    </script>
+
+</html>