mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Removing some files that are no longer used.
This commit is contained in:
James Taylor
Vendored
-4698
File diff suppressed because it is too large
Load Diff
@@ -1,25 +0,0 @@
|
||||
<?xml version="1.0" encoding="utf-8" ?>
|
||||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
||||
<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" />
|
||||
<title>Welcome to Galaxy</title>
|
||||
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
||||
<link rel="stylesheet" href="/static/style/help.css" type="text/css" />
|
||||
</head>
|
||||
<body>
|
||||
<div class="document" id="welcome-to-galaxy">
|
||||
<h1 class="title">Welcome to Galaxy</h1>
|
||||
<p>Galaxy is a web-based data analysis framework for comparative genomics. It exists in two flavors:</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference" href="http://g2.bx.psu.edu:9000">Galaxy2</a> - features genomic datasets and allows various operations on genomic coordinates</li>
|
||||
<li><a class="reference" href="http://galaxy.cse.psu.edu">Galaxy1</a> - the old version that is still maintained but not actively developed</li>
|
||||
</ul>
|
||||
<hr class="docutils" />
|
||||
<p>Galaxy aims to be a zero configuration entirely self contained system, that provides a lightweight webserver, an embedded database and a multi-threaded job manager. Tools (and their parameters) can be specified via simple XML based configuration files. Galaxy allows you to deploy a wide variety of bioinformatics tools through the web. It renders all HTML widgets the tools need, verifies inputs, and stores and manages the outputs that these tools create.</p>
|
||||
<hr class="docutils" />
|
||||
<p><a class="reference" href="http://www.bx.psu.edu">The Center for Comparative Genomics and Bioinformatics</a> at <a class="reference" href="http://www.psu.edu">Penn State</a> | 2005</p>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
@@ -1,23 +0,0 @@
|
||||
Welcome to Galaxy
|
||||
=================
|
||||
|
||||
Galaxy is a web-based data analysis framework for comparative genomics. It exists in two flavors:
|
||||
|
||||
* `Galaxy2`__ - features genomic datasets and allows various operations on genomic coordinates
|
||||
* `Galaxy1`__ - the old version that is still maintained but not actively developed
|
||||
|
||||
.. __: http://g2.bx.psu.edu:9000
|
||||
|
||||
.. __: http://galaxy.cse.psu.edu
|
||||
|
||||
|
||||
-----
|
||||
|
||||
Galaxy aims to be a zero configuration entirely self contained system, that provides a lightweight webserver, an embedded database and a multi-threaded job manager. Tools (and their parameters) can be specified via simple XML based configuration files. Galaxy allows you to deploy a wide variety of bioinformatics tools through the web. It renders all HTML widgets the tools need, verifies inputs, and stores and manages the outputs that these tools create.
|
||||
|
||||
-----
|
||||
|
||||
`The Center for Comparative Genomics and Bioinformatics`__ at `Penn State`__ | 2005
|
||||
|
||||
.. __: http://www.bx.psu.edu
|
||||
.. __: http://www.psu.edu
|
||||
@@ -1,11 +0,0 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Frameset//EN" "http://www.w3.org/TR/html4/frameset.dtd">
|
||||
<HTML>
|
||||
<HEAD>
|
||||
<TITLE>Galaxy</TITLE>
|
||||
</HEAD>
|
||||
<FRAMESET cols="25%,50%,30%" border="3" framespacing="3" frameborder="1">
|
||||
<FRAME name="galaxy_tool_menu" src="../tool_menu" frameborder="0">
|
||||
<FRAME name="galaxy_main" src="welcome.html" frameborder="0">
|
||||
<FRAME name="galaxy_history" src="../history" frameborder="0">
|
||||
</FRAMESET>
|
||||
</HTML>
|
||||
@@ -1,335 +0,0 @@
|
||||
body
|
||||
{
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
border: 0;
|
||||
font: smaller verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;
|
||||
background: #3690c0;
|
||||
}
|
||||
|
||||
body.toolMenuPage
|
||||
{
|
||||
background: #045a8d;
|
||||
color: #d0d1e6;
|
||||
/*background-image: url(/static/images/toolsExpandingMenu.gif);*/
|
||||
background-repeat: no-repeat;
|
||||
background-position: bottom right;
|
||||
}
|
||||
|
||||
body.toolMenuPage a
|
||||
{
|
||||
color: #ece7f2;
|
||||
}
|
||||
|
||||
body.toolMenuPage a:hover
|
||||
{
|
||||
color: white;
|
||||
}
|
||||
|
||||
body.historyPage
|
||||
{
|
||||
background: #045a8d;
|
||||
color: #d0d1e6;
|
||||
/*background-image: url(/static/images/history.gif);*/
|
||||
background-repeat: no-repeat;
|
||||
background-position: bottom right;
|
||||
}
|
||||
|
||||
body.historyPage a
|
||||
{
|
||||
color: #ece7f2;
|
||||
}
|
||||
|
||||
body.mastheadPage
|
||||
{
|
||||
background: #023858;
|
||||
background-image: url(/static/images/hatch-fade-023858.gif);
|
||||
background-position: bottom;
|
||||
color: white;
|
||||
}
|
||||
|
||||
body.mastheadPage a
|
||||
{
|
||||
color: #ece7f2;
|
||||
}
|
||||
|
||||
div.pageTitle
|
||||
{
|
||||
font-size: x-large;
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
div.pageTitle a:link, div.pageTitle a:visited, div.pageTitle a:active, div.pageTitle a:hover
|
||||
{
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
/*
|
||||
6 class diverging BrBG
|
||||
|
||||
br2: #8c510a
|
||||
br1: #d8b365
|
||||
br0: #f6e8c3
|
||||
gr0: #c7eae5
|
||||
gr1: #5ab4ac
|
||||
gr2: #01665e
|
||||
*/
|
||||
|
||||
/*
|
||||
|
||||
Dark to light:
|
||||
|
||||
Blues
|
||||
-----
|
||||
|
||||
0: #023858
|
||||
1: #045a8d
|
||||
3: #0570b0
|
||||
4: #3690c0
|
||||
5: #74a9cf
|
||||
6: #a6bddb
|
||||
7: #d0d1e6
|
||||
8: #ece7f2
|
||||
|
||||
|
||||
*/
|
||||
|
||||
h1, h2, h3
|
||||
{
|
||||
color: white;
|
||||
}
|
||||
|
||||
hr
|
||||
{
|
||||
border: none;
|
||||
border-bottom: dotted white 1px;
|
||||
}
|
||||
|
||||
div.toolMenu
|
||||
{
|
||||
margin: 10px;
|
||||
}
|
||||
|
||||
div.toolDivider
|
||||
{
|
||||
padding-top: 5px;
|
||||
padding-bottom: 5px;
|
||||
}
|
||||
|
||||
div.toolSectionDetailsInner
|
||||
{
|
||||
margin-left: 10px;
|
||||
margin-right: 10px;
|
||||
}
|
||||
|
||||
div.toolSectionTitle
|
||||
{
|
||||
padding-bottom: 5px;
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
/*div.toolSectionBg
|
||||
{
|
||||
background: #0570b0;
|
||||
}*/
|
||||
|
||||
div.toolTitle
|
||||
{
|
||||
padding-top: 5px;
|
||||
padding-bottom: 5px;
|
||||
margin-left: 16px;
|
||||
margin-right: 10px;
|
||||
display: list-item;
|
||||
list-style: square outside;
|
||||
}
|
||||
|
||||
div.toolForm
|
||||
{
|
||||
margin: 10px;
|
||||
}
|
||||
|
||||
div.toolFormTitle
|
||||
{
|
||||
background: #d8b365;
|
||||
font-weight: bold;
|
||||
padding: 5px;
|
||||
}
|
||||
|
||||
div.toolParamHelp
|
||||
{
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
div.toolFormBody
|
||||
{
|
||||
background: #f6e8c3;
|
||||
padding: 5px;
|
||||
}
|
||||
|
||||
td.errorMessage
|
||||
{
|
||||
color: #b30000;
|
||||
}
|
||||
|
||||
div.toolHelp
|
||||
{
|
||||
margin: 10px;
|
||||
}
|
||||
|
||||
div.toolHelpBody
|
||||
{
|
||||
background: white;
|
||||
padding: 5px;
|
||||
}
|
||||
|
||||
div.historyItem
|
||||
{
|
||||
padding-top: 10px;
|
||||
padding-bottom: 10px;
|
||||
margin-right: 10px;
|
||||
margin-left: 10px;
|
||||
border-bottom: dotted #d0d1e6 1px;
|
||||
}
|
||||
|
||||
div.historyItemBody div
|
||||
{
|
||||
padding-top: 2px;
|
||||
}
|
||||
|
||||
pre.peek
|
||||
{
|
||||
background: #f6e8c3;
|
||||
color: black;
|
||||
width: 100%;
|
||||
overflow: auto;
|
||||
}
|
||||
|
||||
div.document
|
||||
{
|
||||
margin: 10px;
|
||||
}
|
||||
|
||||
select
|
||||
{
|
||||
max-width: 300px;
|
||||
}
|
||||
|
||||
.errormessage, .warningmessage, .donemessage, .infomessage
|
||||
{
|
||||
margin: 10px;
|
||||
padding: .33em 0 .67em 42px;
|
||||
min-height: 32px;
|
||||
border-top: 5px solid #900;
|
||||
border-bottom: 5px solid #900;
|
||||
/* border-left: 1px solid #900; */
|
||||
/* border-right: 1px solid #900; */
|
||||
background: white;
|
||||
background-image: url(/images/icon_error_lrg.gif);
|
||||
background-repeat: no-repeat;
|
||||
background-position: 5px 5px;
|
||||
}
|
||||
|
||||
.warningmessage
|
||||
{
|
||||
background-image: url(/images/icon_warning_lrg.gif);
|
||||
border-color: #c60;
|
||||
}
|
||||
|
||||
.donemessage
|
||||
{
|
||||
background-image: url(/images/icon_success_lrg.gif);
|
||||
border-color: #090;
|
||||
}
|
||||
|
||||
.infomessage
|
||||
{
|
||||
background-image: url(/images/icon_info_lrg.gif);
|
||||
border-color: #069;
|
||||
}
|
||||
|
||||
.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr
|
||||
{
|
||||
padding-left: 20px;
|
||||
min-height: 15px;
|
||||
background: url(/images/icon_error_sml.gif) no-repeat;
|
||||
}
|
||||
|
||||
.warningmark
|
||||
{
|
||||
background-image: url(/images/icon_warning_sml.gif);
|
||||
}
|
||||
|
||||
.donemark
|
||||
{
|
||||
background-image: url(/images/icon_success_sml.gif);
|
||||
}
|
||||
|
||||
.infomark, .ok_bgr
|
||||
{
|
||||
background-image: url(/images/icon_info_sml.gif);
|
||||
}
|
||||
|
||||
table.colored td
|
||||
{
|
||||
padding: 5px;
|
||||
}
|
||||
|
||||
table.colored tr.header
|
||||
{
|
||||
background: #d8b365;
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
table.colored tr
|
||||
{
|
||||
background: #f6e8c3;
|
||||
}
|
||||
|
||||
div.debug
|
||||
{
|
||||
margin: 10px;
|
||||
padding: 5px;
|
||||
background: #FFFF99;
|
||||
border: solid #FFFF33 1px;
|
||||
color: black;
|
||||
}
|
||||
|
||||
#footer {
|
||||
position: fixed;
|
||||
background: #023858;
|
||||
width: 100%;
|
||||
left: 0px;
|
||||
bottom: 0px;
|
||||
color: white;
|
||||
z-index:10000;
|
||||
opacity:0.9;
|
||||
filter:alpha(opacity:90);
|
||||
}
|
||||
|
||||
.footerheader
|
||||
{
|
||||
padding: 5px;
|
||||
text-align:center;
|
||||
background-image: url(/static/images/hatch-fade-023858.gif);
|
||||
background-position: bottom;
|
||||
}
|
||||
|
||||
.footermenu
|
||||
{
|
||||
border-top: solid white 1px;
|
||||
}
|
||||
|
||||
.footermenuitem
|
||||
{
|
||||
margin-top: 5px;
|
||||
margin-bottom: 5px;
|
||||
margin-right: 5px;
|
||||
margin-left: 25px;
|
||||
display: list-item;
|
||||
list-style: square outside;
|
||||
}
|
||||
|
||||
.footermenumessage
|
||||
{
|
||||
margin: 5px;
|
||||
}
|
||||
@@ -1,3 +0,0 @@
|
||||
function main(){
|
||||
|
||||
}
|
||||
@@ -1,180 +0,0 @@
|
||||
body {
|
||||
margin-top: 10px;
|
||||
margin-left: 50px;
|
||||
margin-right: 30px;
|
||||
padding: 0;
|
||||
border: 0;
|
||||
font: smaller verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;
|
||||
}
|
||||
|
||||
a {text-decoration: underline}
|
||||
a:link {text-decoration: underline}
|
||||
a:visited {text-decoration: underline}
|
||||
a:active {text-decoration: none}
|
||||
a:hover {text-decoration: underline; background: #CCCCFF}
|
||||
|
||||
.indent1 {
|
||||
margin-left: 30px;
|
||||
}
|
||||
|
||||
.tool_area {
|
||||
margin:10px;
|
||||
margin-left: 30px;
|
||||
}
|
||||
|
||||
.tool_name a {
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
.tool_form {
|
||||
background-color: #FFFFCC;
|
||||
border: 1px solid #EEEEEE;
|
||||
margin: 5px;
|
||||
}
|
||||
|
||||
.info {
|
||||
color: #990000;
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
.border {
|
||||
border: 1px solid #8cacbb;
|
||||
background: #FFFFFF;
|
||||
}
|
||||
|
||||
.rline {
|
||||
border-bottom: 1px solid #EEEEEE;
|
||||
}
|
||||
|
||||
.bline {
|
||||
border-bottom: 1px solid #999999;
|
||||
}
|
||||
|
||||
.tline {
|
||||
padding-top: 5pt;
|
||||
border-top: 1px solid #999999;
|
||||
}
|
||||
|
||||
.grey {
|
||||
border: 1px #FFFFFF solid;
|
||||
}
|
||||
|
||||
.greyborder {
|
||||
background: #EFEFEF;
|
||||
border: 1px #CCCCCC solid;
|
||||
}
|
||||
|
||||
.big { font-size: large; font-weight: bold; color: #000066}
|
||||
.mark {color: #CC3300}
|
||||
|
||||
.smaller {font-size: smaller}
|
||||
.larger {font-size: larger}
|
||||
|
||||
.larger {font-size: larger; color: #000066}
|
||||
.head {
|
||||
font-size: large;
|
||||
font-weight: bold;
|
||||
color: #CC0000;
|
||||
}
|
||||
|
||||
.ok_bgr {
|
||||
background: #AEFF5E;
|
||||
border: 1px #76EC00 solid;
|
||||
border-color: #66CC00 #66CC00 #66CC00 #66CC00;
|
||||
}
|
||||
|
||||
.err_bgr {
|
||||
background: #FFCE7B;
|
||||
border: 1px solid #FFA500;
|
||||
border-color:#FFA500 #FFA500 #FFA500 #FFA500;
|
||||
}
|
||||
|
||||
.grey {
|
||||
background: #EFEFEF;
|
||||
}
|
||||
|
||||
.greyborder {
|
||||
background: #EFEFEF;
|
||||
border: 1px #CCCCCC solid;
|
||||
}
|
||||
|
||||
|
||||
.utextarea {
|
||||
font: 110% "Courier New", Courier, monospace;
|
||||
border: 1px solid #8cacbb;
|
||||
color: Black;
|
||||
background-color: white;
|
||||
width: 95%;
|
||||
padding: 5pt;
|
||||
}
|
||||
.uinput {
|
||||
font-family: "Lucida Grande", Verdana, Lucida, Helvetica, Arial, sans-serif;
|
||||
visibility: visible;
|
||||
border: 1px solid #8cacbb;
|
||||
color: Black;
|
||||
background-color: white;
|
||||
vertical-align: middle;
|
||||
}
|
||||
|
||||
.hg17 { color: #FF6600; }
|
||||
.hg16 { color: #02AC20; }
|
||||
.bed { color: #009999; }
|
||||
.xbed { color: #006666; }
|
||||
.txt { color: #0066FF; }
|
||||
.text { color: #0066FF; }
|
||||
.png { color: #33CC33; }
|
||||
.gif { color: #009900; }
|
||||
.html { color: #3399FF; }
|
||||
.htm { color: #3399FF; }
|
||||
.jpg { color: #006600; }
|
||||
.jpeg { color: #006600; }
|
||||
.fasta { color: #0066CC; }
|
||||
.pdf { color: #003366; }
|
||||
.wig { color: #3366CC; }
|
||||
.gff { color: #0000FF; }
|
||||
.fa { color: #FF3333; }
|
||||
.acedb { color: #FF6666; }
|
||||
.asn1 { color: #CC6666; }
|
||||
.clustal { color: #993333; }
|
||||
.codata { color: #FF0000; }
|
||||
.embl { color: #009999; }
|
||||
.fitch { color: #FF3300; }
|
||||
.gcg { color: #66CC00; }
|
||||
.genbank { color: #999900; }
|
||||
.hennig86 { color: #666633; }
|
||||
.ig { color: #CCCC99; }
|
||||
.jackknifer { color: #FFCC99; }
|
||||
.jackknifernon { color: #FFCC99; }
|
||||
.mega { color: #99FF00; }
|
||||
.meganon { color: #99FF00; }
|
||||
.msf { color: #66FF33; }
|
||||
.pir { color: #009933; }
|
||||
.ncbi { color: #339933; }
|
||||
.nexus { color: #009900; }
|
||||
.nexusnon { color: #CCFF99; }
|
||||
.phylip { color: #99CC66; }
|
||||
.phylipnon { color: #336600; }
|
||||
.selex { color: #99FF33; }
|
||||
.staden { color: #00CC66; }
|
||||
.strider { color: #33FF99; }
|
||||
.swiss { color: #006633; }
|
||||
.dbmotif { color: #339966; }
|
||||
.diffseq { color: #66CC99; }
|
||||
.excel { color: #99FFCC; }
|
||||
.feattable { color: #99CCFF; }
|
||||
.motif { color: #6699CC; }
|
||||
.regions { color: #336699; }
|
||||
.seqtable { color: #663300; }
|
||||
.simple { color: #996633; }
|
||||
.srs { color: #CC9966; }
|
||||
.table { color: #CC6600; }
|
||||
.tagseq { color: #FF9933; }
|
||||
.pair { color: #FFCC66; }
|
||||
.markx0 { color: #CC9933; }
|
||||
.markx1 { color: #CC9933; }
|
||||
.markx2 { color: #CC9933; }
|
||||
.markx3 { color: #CC9933; }
|
||||
.markx10 { color: #CC9933; }
|
||||
.srspair { color: #CC9966; }
|
||||
.score { color: #663333; }
|
||||
.nametable { color: #00CC33; }
|
||||
@@ -1,163 +0,0 @@
|
||||
var open_ids = []
|
||||
var cookie_name = "universe_ui"
|
||||
var now = new Date();
|
||||
now.setTime(now.getTime() + 365 * 24 * 60 * 60 * 1000);
|
||||
|
||||
//
|
||||
// cookie management off the web
|
||||
// http://www.webreference.com/js/column8/property.html
|
||||
//
|
||||
function setCookie(name, value, expires, path, domain, secure) {
|
||||
var curCookie = name + "=" + escape(value) +
|
||||
((expires) ? "; expires=" + expires.toGMTString() : "") +
|
||||
((path) ? "; path=" + path : "") +
|
||||
((domain) ? "; domain=" + domain : "") +
|
||||
((secure) ? "; secure" : "");
|
||||
document.cookie = curCookie;
|
||||
}
|
||||
|
||||
function getCookie(name) {
|
||||
var dc = document.cookie;
|
||||
var prefix = name + "=";
|
||||
var begin = dc.indexOf("; " + prefix);
|
||||
if (begin == -1) {
|
||||
begin = dc.indexOf(prefix);
|
||||
if (begin != 0) return null;
|
||||
} else
|
||||
begin += 2;
|
||||
var end = document.cookie.indexOf(";", begin);
|
||||
if (end == -1)
|
||||
end = dc.length;
|
||||
return unescape(dc.substring(begin + prefix.length, end));
|
||||
}
|
||||
|
||||
|
||||
function main(){
|
||||
init_ids()
|
||||
//debugger
|
||||
for (i=0; i<len(open_ids); i++){
|
||||
value = open_ids[i]
|
||||
expand_basic(value)
|
||||
}
|
||||
}
|
||||
|
||||
function toggle_value(value) {
|
||||
// everything starts out closed
|
||||
var found = 0
|
||||
var tmp_list = []
|
||||
for (i=0; i<len(open_ids); i++){
|
||||
id = open_ids[i]
|
||||
if ( id == value) {
|
||||
found = 1
|
||||
} else {
|
||||
tmp_list.push(id)
|
||||
}
|
||||
}
|
||||
|
||||
if (found) {
|
||||
open_ids = tmp_list
|
||||
} else {
|
||||
open_ids.push(value)
|
||||
}
|
||||
|
||||
cookie_value = open_ids.join(':')
|
||||
setCookie(cookie_name, cookie_value, now)
|
||||
}
|
||||
|
||||
function init_ids() {
|
||||
var value = getCookie(cookie_name);
|
||||
if (value) {
|
||||
var items = value.split(":")
|
||||
for (i=0; i<len(items); i++){
|
||||
id = items[i]
|
||||
elem = get(id)
|
||||
if (elem) {
|
||||
open_ids.push(id)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// this expands without the toggle
|
||||
function expand_basic(name){
|
||||
var elem = get(name)
|
||||
if (elem) {
|
||||
if (elem.style.display=="none"){
|
||||
elem.style.display="block"
|
||||
} else {
|
||||
elem.style.display="none"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
//this collapses all known open things
|
||||
function collapse_all(){
|
||||
var cur_open = open_ids
|
||||
for (var i=0; i<len(cur_open); i++){
|
||||
expand(cur_open[i])
|
||||
}
|
||||
}
|
||||
|
||||
// this toggles between none and block
|
||||
function expand(name){
|
||||
var elem = get(name)
|
||||
if (elem) {
|
||||
if (elem.style.display=="none"){
|
||||
elem.style.display="block"
|
||||
} else {
|
||||
elem.style.display="none"
|
||||
}
|
||||
toggle_value(name)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// this toggles between visible and hidden
|
||||
function show(name){
|
||||
var elem = get(name)
|
||||
if (elem.style.visibility=="hidden"){
|
||||
elem.style.visibility="visible";
|
||||
} else {
|
||||
elem.style.visibility="hidden";
|
||||
}
|
||||
}
|
||||
|
||||
// utility function to get the length of on object
|
||||
function len(obj){
|
||||
return obj.length;
|
||||
}
|
||||
|
||||
// utility function to get an element by id
|
||||
function get(name){
|
||||
return document.getElementById(name);
|
||||
}
|
||||
|
||||
// pops up a window
|
||||
function pop_up(url) {
|
||||
day = new Date();
|
||||
id = day.getTime();
|
||||
eval("page" + id + " = window.open(url, '" + id + "', 'toolbar=0,scrollbars=1,location=0,statusbar=1,menubar=0,resizable=1,width=500,height=300');");
|
||||
}
|
||||
|
||||
function frame_up(){
|
||||
obj = parent.document.getElementById('inner')
|
||||
if (obj) {
|
||||
obj.setAttribute('rows', '30%,70%', 0);
|
||||
}
|
||||
}
|
||||
|
||||
function frame_dw(){
|
||||
obj = parent.document.getElementById('inner')
|
||||
if (obj) {
|
||||
obj.setAttribute('rows', '70%,30%', 0);
|
||||
}
|
||||
}
|
||||
|
||||
// Confirm History Delete
|
||||
function confirm_click(url){
|
||||
response = confirm("Are you sure you want to delete this history?")
|
||||
if (response != 0)
|
||||
{
|
||||
location = url
|
||||
}
|
||||
}
|
||||
@@ -1,95 +0,0 @@
|
||||
dojo.require("dojo.animation");
|
||||
|
||||
function wipeIn_dojo(node, duration, callback, dontPlay)
|
||||
{
|
||||
// Determine the full height of the element
|
||||
node.style.overflow = "visible";
|
||||
node.style.visibility = "hidden";
|
||||
// Prevents a flicker on mozilla
|
||||
if ( dojo.render.html.mozilla )
|
||||
{
|
||||
node.style.position = "absolute";
|
||||
}
|
||||
node.style.display = "block";
|
||||
var height = node.offsetHeight;
|
||||
// Restore
|
||||
node.style.display = "none";
|
||||
node.style.position = "";
|
||||
node.style.visibility = "";
|
||||
|
||||
var anim = wipeInToHeight(node, duration, height, function(e) {
|
||||
node.style.height = "auto";
|
||||
node.style.display = "block";
|
||||
if(callback) { callback(node, anim); }
|
||||
}, dontPlay);
|
||||
};
|
||||
|
||||
function wipeInToHeight(node, duration, height, callback, dontPlay)
|
||||
{
|
||||
var savedOverflow = dojo.html.getStyle(node, "overflow");
|
||||
node.style.display = "none";
|
||||
node.style.height = 0;
|
||||
if(savedOverflow == "visible") {
|
||||
node.style.overflow = "hidden";
|
||||
}
|
||||
node.style.display = "block";
|
||||
|
||||
var anim = new dojo.animation.Animation(
|
||||
new dojo.math.curves.Line([0], [height]),
|
||||
duration, 0);
|
||||
dojo.event.connect(anim, "onAnimate", function(e) {
|
||||
node.style.height = Math.round(e.x) + "px";
|
||||
});
|
||||
dojo.event.connect(anim, "onEnd", function(e) {
|
||||
if(savedOverflow != "visible") {
|
||||
node.style.overflow = savedOverflow;
|
||||
}
|
||||
if(callback) { callback(node, anim); }
|
||||
});
|
||||
if( !dontPlay ) { anim.play(true); }
|
||||
return anim;
|
||||
}
|
||||
|
||||
function wipeOut_dojo(node, duration, callback, dontPlay)
|
||||
{
|
||||
var savedOverflow = dojo.html.getStyle(node, "overflow");
|
||||
var savedHeight = dojo.html.getStyle(node, "height");
|
||||
var height = node.offsetHeight;
|
||||
node.style.overflow = "hidden";
|
||||
|
||||
var anim = new dojo.animation.Animation(
|
||||
new dojo.math.curves.Line([height], [0]),
|
||||
duration, 0);
|
||||
dojo.event.connect(anim, "onAnimate", function(e) {
|
||||
node.style.height = Math.round(e.x) + "px";
|
||||
});
|
||||
dojo.event.connect(anim, "onEnd", function(e) {
|
||||
node.style.display = "none";
|
||||
node.style.overflow = savedOverflow;
|
||||
node.style.height = savedHeight || "auto";
|
||||
if(callback) { callback(node, anim); }
|
||||
});
|
||||
if( !dontPlay ) { anim.play(true); }
|
||||
return anim;
|
||||
};
|
||||
|
||||
function wipeIn_simple( node, duration )
|
||||
{
|
||||
node.style.display = "block";
|
||||
}
|
||||
|
||||
function wipeOut_simple( node, duration )
|
||||
{
|
||||
node.style.display = "none";
|
||||
}
|
||||
|
||||
if ( dojo.render.html.safari || dojo.render.html.mozilla || dojo.render.html.ie60 )
|
||||
{
|
||||
wipeIn = wipeIn_dojo;
|
||||
wipeOut = wipeOut_dojo;
|
||||
}
|
||||
else
|
||||
{
|
||||
wipeIn = wipeIn_simple;
|
||||
wipeOut = wipeOut_simple;
|
||||
}
|
||||
@@ -1,196 +0,0 @@
|
||||
<% _=n_ %>
|
||||
<%inherit file="/base.mako"/>
|
||||
<%def name="title()">${_('Your saved histories')}</%def>
|
||||
|
||||
%if message:
|
||||
<p>
|
||||
<div class="${message_type}message transient-message">${message}</div>
|
||||
<div style="clear: both"></div>
|
||||
</p>
|
||||
%endif
|
||||
|
||||
<%def name="javascripts()">
|
||||
${parent.javascripts()}
|
||||
<script type="text/javascript">
|
||||
%if refresh_history:
|
||||
if ( parent.frames && parent.frames.galaxy_history ) {
|
||||
parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
|
||||
}
|
||||
%endif
|
||||
|
||||
## TODO: generalize and move into galaxy.base.js
|
||||
$(function() {
|
||||
$(".grid").each( function() {
|
||||
var grid = this;
|
||||
var checkboxes = $(this).find("input.grid-row-select-checkbox");
|
||||
var update = $(this).find( "span.grid-selected-count" );
|
||||
$(checkboxes).each( function() {
|
||||
$(this).change( function() {
|
||||
var n = $(checkboxes).filter("[checked]").size();
|
||||
update.text( n );
|
||||
});
|
||||
})
|
||||
});
|
||||
});
|
||||
|
||||
</script>
|
||||
</%def>
|
||||
|
||||
<%def name="stylesheets()">
|
||||
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
|
||||
<style>
|
||||
.count-box {
|
||||
width: 1.1em;
|
||||
float: left;
|
||||
padding: 5px;
|
||||
margin-right: 5px;
|
||||
border-width: 1px;
|
||||
border-style: solid;
|
||||
text-align: center;
|
||||
}
|
||||
.count-box-dummy {
|
||||
width: 1.1em;
|
||||
float: left;
|
||||
padding: 5px;
|
||||
margin-right: 5px;
|
||||
border-width: 1px;
|
||||
border-style: solid;
|
||||
border-color: transparent;
|
||||
background: transparent;
|
||||
text-align: center;
|
||||
}
|
||||
</style>
|
||||
</%def>
|
||||
|
||||
|
||||
<h2>${_('Stored Histories')}</h2>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
%if show_deleted:
|
||||
<a href="${h.url_for( show_deleted=False )}" class="action-button">${_('Hide deleted')}</a></div>
|
||||
%else:
|
||||
<a href="${h.url_for( show_deleted=True )}" class="action-button">${_('Show deleted')}</a></div>
|
||||
%endif
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<form name="history_actions" action="${h.url_for()}" method="post" >
|
||||
%if show_deleted:
|
||||
<input type="hidden" name="show_deleted" value="true">
|
||||
%endif
|
||||
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th width="1.5em"></th>
|
||||
<th>Name (click to activate)</th>
|
||||
<th>Datasets (by state)</th>
|
||||
<th>Status</th>
|
||||
<th>Last update</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
</thead>
|
||||
|
||||
<tbody>
|
||||
|
||||
%for i, history in enumerate( user.histories ):
|
||||
|
||||
%if ( show_deleted and not history.purged ) or not( history.deleted ):
|
||||
|
||||
<tr class="${["","current"][ history == trans.get_history() ]}">
|
||||
|
||||
<td><input type="checkbox" name="id" value="${history.id}" class="grid-row-select-checkbox"></td>
|
||||
|
||||
<td>
|
||||
%if not history.deleted:
|
||||
<a href="${h.url_for( operation="switch", id=history.id, show_deleted=show_deleted )}">${history.name}</a>
|
||||
<a id="h-${i}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
%else:
|
||||
${history.name} <a id="h-${i}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
%endif
|
||||
</td>
|
||||
|
||||
<td>
|
||||
|
||||
<%
|
||||
total_ok = sum( 1 for d in history.active_datasets if d.state == 'ok' )
|
||||
total_running = sum( 1 for d in history.active_datasets if d.state == 'running' )
|
||||
total_queued = sum( 1 for d in history.active_datasets if d.state == 'queued' )
|
||||
total_error = sum( 1 for d in history.active_datasets if d.state == 'error' )
|
||||
%>
|
||||
|
||||
%if total_ok:
|
||||
<div class="count-box state-color-ok">${total_ok}</div>
|
||||
%else:
|
||||
<div class="count-box-dummy"></div>
|
||||
%endif
|
||||
|
||||
%if total_error:
|
||||
<div class="count-box state-color-error">${total_error}</div
|
||||
%else:
|
||||
<div class="count-box-dummy"></div>
|
||||
%endif
|
||||
|
||||
%if total_running:
|
||||
<div class="count-box state-color-running">${total_running}</div>
|
||||
%else:
|
||||
<div class="count-box-dummy"></div>
|
||||
%endif
|
||||
|
||||
%if total_queued:
|
||||
<div class="count-box state-color-queued">${total_queued}</div>
|
||||
%else:
|
||||
<div class="count-box-dummy"></div>
|
||||
%endif
|
||||
|
||||
</td>
|
||||
|
||||
<td>
|
||||
%if history == trans.get_history():
|
||||
active
|
||||
%endif
|
||||
%if history.deleted:
|
||||
deleted
|
||||
%endif
|
||||
</td>
|
||||
|
||||
<td>${h.date.distance_of_time_in_words( history.update_time, h.date.datetime.utcnow() )}</td>
|
||||
|
||||
<td>
|
||||
<div popupmenu="h-${i}-popup">
|
||||
|
||||
%if not history.deleted:
|
||||
<a class="action-button" href="${h.url_for( operation='rename', id=history.id, show_deleted=show_deleted )}">${_('rename')}</a> <br />
|
||||
<a class="action-button" href="${h.url_for( operation='switch', id=history.id, show_deleted=show_deleted )}">${_('switch to')}</a> <br />
|
||||
<a class="action-button" href="${h.url_for( operation='delete', id=history.id , show_deleted=show_deleted)}" confirm="Are you sure you want to delete this history?">${_('delete')}</a> <br />
|
||||
%else:
|
||||
<a class="action-button" href="${h.url_for( operation='undelete', id=history.id, show_deleted=show_deleted )}">${_('undelete')}</a><br />
|
||||
%endif
|
||||
|
||||
</div>
|
||||
</td>
|
||||
|
||||
</tr>
|
||||
|
||||
%endif
|
||||
|
||||
%endfor
|
||||
|
||||
</tbody>
|
||||
<tfoot>
|
||||
<tr>
|
||||
<td></td>
|
||||
<td colspan="6">
|
||||
For <span class="grid-selected-count"></span> selected histories:
|
||||
<input type="submit" name="operation" value="Share" class="action-button">
|
||||
<input type="submit" name="operation" value="Rename" class="action-button">
|
||||
<input type="submit" name="operation" value="Delete" class="action-button">
|
||||
%if show_deleted:
|
||||
<input type="submit" name="operation" value="${_('Undelete')}" class="action-button">
|
||||
%endif
|
||||
</td>
|
||||
</tr>
|
||||
</tfoot>
|
||||
</table>
|
||||
</form>
|
||||
@@ -1,83 +0,0 @@
|
||||
<% _=n_ %>
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
<title>Galaxy</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; ${_('iso-8859-1')}" />
|
||||
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
|
||||
<link href="${h.url_for('/static/style/masthead.css')}" rel="stylesheet" type="text/css" />
|
||||
</head>
|
||||
|
||||
<body class="mastheadPage" scroll="no">
|
||||
<div id="tab-bar-bottom"></div>
|
||||
<table height="32" width="100%" cellspacing="0" border="0">
|
||||
<tr valign="middle"><td width="26px"><a target="_blank" href="${wiki_url}">
|
||||
<img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"></a></td>
|
||||
<td align="left" valign="middle"><div class="pageTitle">Galaxy${brand}</div></td>
|
||||
<td align="right" valign="middle">
|
||||
%if not app.config.require_login or ( app.config.require_login and trans.user):
|
||||
View: <span class="link-group">
|
||||
<span
|
||||
%if active_view == "analysis":
|
||||
class="active-link"
|
||||
%endif
|
||||
><a target="_parent" href="${h.url_for( controller='root', action='index' )}">analysis</a></span>
|
||||
| <span
|
||||
%if active_view == "workflow":
|
||||
class="active-link"
|
||||
%endif
|
||||
><a target="_parent" href="${h.url_for( controller='workflow', action='index' )}">workflow</a></span>
|
||||
| <span
|
||||
%if active_view == "libraries":
|
||||
class="active-link"
|
||||
%endif
|
||||
><a target="_parent" href="${h.url_for( controller='library', action='index' )}">libraries</a></span>
|
||||
%if admin_user == "true":
|
||||
| <span
|
||||
%if active_view == "admin":
|
||||
class="active-link"
|
||||
%endif
|
||||
><a target="_parent" href="${h.url_for( controller='admin', action='index' )}">admin</a></span>
|
||||
%endif
|
||||
|
||||
</span>
|
||||
|
||||
%endif
|
||||
<span class="link-group">
|
||||
Info: <span><a href="${bugs_email}">report bugs</a></span>
|
||||
| <span><a target="_blank" href="${wiki_url}">wiki</a></span>
|
||||
| <span><a target="_blank" href="${screencasts_url}">screencasts</a></span>
|
||||
</span>
|
||||
<!-- | <a target="mainframe" href="/static/index_frame_tools.html">tools</a>
|
||||
| <a target="mainframe" href="/static/index_frame_history.html">history</a> -->
|
||||
|
||||
<span class="link-group">
|
||||
%if app.config.use_remote_user:
|
||||
Logged in as ${t.user.email}
|
||||
%else:
|
||||
%if t.user:
|
||||
Logged in as ${t.user.email}: <span><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">manage</a></span>
|
||||
%if app.config.require_login:
|
||||
| <span><a target="_parent" href="${h.url_for( controller='root', action='index', m_c='user', m_a='logout' )}">logout</a></span>
|
||||
%else:
|
||||
| <span><a target="galaxy_main" href="${h.url_for( controller='user', action='logout' )}">logout</a></span>
|
||||
%endif
|
||||
%else:
|
||||
Account:
|
||||
%if app.config.allow_user_creation:
|
||||
<span><a target="galaxy_main" href="${h.url_for( controller='user', action='create' )}">create</a></span> |
|
||||
%endif
|
||||
<span><a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">login</a></span>
|
||||
%endif
|
||||
%endif
|
||||
|
||||
</span>
|
||||
</td>
|
||||
</tr>
|
||||
</table>
|
||||
</body>
|
||||
|
||||
</html>
|
||||
|
||||
Reference in New Issue
Block a user