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anuprulez
2017-03-28 17:22:44 +02:00
parent 876c7a2d3d 66ca698f5a
commit 8e1d761bec
35 changed files with 1625 additions and 582 deletions
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config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
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@@ -0,0 +1,11 @@
# This file lists acceptable images to allow runing.
#
# This allows you, the admin, to create multiple flavours
# for your users to run. E.g. maybe you need a geosciences flavour,
# you can create the image based on our default image and add the
# appropriate `apt-get/pip install` statements.
---
-
image: shiltemann/ethercalc-galaxy-ie:17.05
description: |
EtherCalc is a web spreadsheet.
config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
-3
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@@ -12,9 +12,6 @@
# usual group/sudo changes.
#command = docker {docker_args}
# The docker image name that should be started.
image = shiltemann/ethercalc-galaxy-ie:17.05
# Additional arguments that are passed to the `docker run` command.
#command_inject = --sig-proxy=true -e DEBUG=false
config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
+1
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@@ -236,6 +236,7 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
};
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 2 */
/***/ function(module, exports, __webpack_require__) {
config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
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config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
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config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
-1
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config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
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config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
+1
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config/plugins/visualizations/charts/static/repository/build/registry.js
+83 -4
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@@ -44,7 +44,7 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
/* 0 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() { return {nvd3_bar:__webpack_require__( 3 ), nvd3_bar_horizontal:__webpack_require__( 6 ), nvd3_bar_horizontal_stacked:__webpack_require__( 7 ), nvd3_bar_stacked:__webpack_require__( 8 ), nvd3_line:__webpack_require__( 9 ), nvd3_line_focus:__webpack_require__( 10 ), nvd3_scatter:__webpack_require__( 11 ), nvd3_stackedarea:__webpack_require__( 12 ), nvd3_stackedarea_full:__webpack_require__( 13 ), nvd3_stackedarea_stream:__webpack_require__( 14 ), nvd3_pie:__webpack_require__( 15 ), nvd3_histogram:__webpack_require__( 16 ), nvd3_histogram_discrete:__webpack_require__( 17 ), jqplot_bar:__webpack_require__( 18 ), jqplot_boxplot:__webpack_require__( 20 ), jqplot_histogram_discrete:__webpack_require__( 21 ), jqplot_line:__webpack_require__( 22 ), jqplot_scatter:__webpack_require__( 23 ), biojs_msa:__webpack_require__( 24 ), biojs_drawrnajs:__webpack_require__( 25 ), biojs_phylocanvas:__webpack_require__( 26 ), others_example:__webpack_require__( 27 ), others_heatmap:__webpack_require__( 28 ), others_heatmap_cluster:__webpack_require__( 29 ), cytoscape_basic:__webpack_require__( 30 ), pv_viewer:__webpack_require__( 31 ), benfred_venn:__webpack_require__( 32 ), ngl_viewer:__webpack_require__( 33 ),} }.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() { return {nvd3_bar:__webpack_require__( 3 ), nvd3_bar_horizontal:__webpack_require__( 6 ), nvd3_bar_horizontal_stacked:__webpack_require__( 7 ), nvd3_bar_stacked:__webpack_require__( 8 ), nvd3_line:__webpack_require__( 9 ), nvd3_line_focus:__webpack_require__( 10 ), nvd3_scatter:__webpack_require__( 11 ), nvd3_stackedarea:__webpack_require__( 12 ), nvd3_stackedarea_full:__webpack_require__( 13 ), nvd3_stackedarea_stream:__webpack_require__( 14 ), nvd3_pie:__webpack_require__( 15 ), nvd3_histogram:__webpack_require__( 16 ), nvd3_histogram_discrete:__webpack_require__( 17 ), jqplot_bar:__webpack_require__( 18 ), jqplot_boxplot:__webpack_require__( 20 ), jqplot_histogram_discrete:__webpack_require__( 21 ), jqplot_line:__webpack_require__( 22 ), jqplot_scatter:__webpack_require__( 23 ), biojs_msa:__webpack_require__( 24 ), biojs_drawrnajs:__webpack_require__( 25 ), biojs_phylocanvas:__webpack_require__( 26 ), others_example:__webpack_require__( 27 ), others_heatmap:__webpack_require__( 28 ), others_heatmap_cluster:__webpack_require__( 29 ), cytoscape_viewer:__webpack_require__( 30 ), pv_viewer:__webpack_require__( 31 ), benfred_venn:__webpack_require__( 32 ), ngl_viewer:__webpack_require__( 33 ),} }.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 1 */,
@@ -897,14 +897,93 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {
return {
title : 'Cytoscape (Default)',
title : 'Cytoscape',
library : 'Cytoscape',
datatypes : [ 'json' ],
datatypes : [ 'sif', 'json' ],
keywords : 'cytoscape graph nodes edges',
description : 'Basic Cytoscape viewer for connected graphs hosted at http://js.cytoscape.org.'
description : 'A viewer based on graph theory/ network library for analysis and visualisation hosted at http://js.cytoscape.org.',
settings : {
curve_style : {
label : 'Curve style',
help : 'Select a curving method used to separate two or more edges between two nodes.',
type : 'select',
display : 'radio',
value : 'haystack',
data : [ { label : 'Haystack', value : 'haystack' },
{ label : 'Bezier', value : 'bezier' },
{ label : 'Unbundled bezier', value : 'unbundled-bezier' },
{ label : 'Segments', value: 'segments' } ]
},
layout_name : {
label : 'Layout name',
help : 'Select a kind of position of nodes in graph.',
type : 'select',
display : 'radio',
value : 'haystack',
data : [ { label : 'Breadth First', value : 'breadthfirst' },
{ label : 'Circle', value : 'circle' },
{ label : 'Concentric', value : 'concentric' },
{ label : 'Cose', value : 'cose' },
{ label : 'Grid', value : 'grid' },
{ label : 'Null', value: 'null' },
{ label : 'Preset', value : 'preset' },
{ label : 'Random', value : 'random' } ]
},
directed : {
label : 'Directed/Undirected',
help : 'Select a kind of edge.',
type : 'select',
display : 'radio',
value : '',
data : [ { label : 'Directed', value : 'triangle' },
{ label : 'Undirected', value : '' } ]
},
search_algorithm : {
label : 'Graph algorithms',
help : 'Select a search algorithm. For Breadth First Search and Depth First Search, please click on any node of the graph. For A*, please click on two nodes, one for the root and another for the destination.',
type : 'select',
display : 'radio',
value : '',
data : [ { label : 'Breadth First Search', value : 'bfs' },
{ label : 'Depth First Search', value : 'dfs' },
{ label : 'Minimum Spanning Tree (Kruskal)', value : 'kruskal' },
{ label : 'A*', value : 'astar' },
{ label : 'None', value : '' } ]
},
graph_traversal: {
label : 'Graph traversal',
help : 'To select a graph traversal type, please click on any node of the graph',
type : 'select',
display : 'radio',
value : '',
data : [ { label : 'Successors', value : 'successors' },
{ label : 'Predecessors', value : 'predecessors' },
{ label : 'Outgoers', value : 'outgoers' },
{ label : 'Incomers', value : 'incomers' },
{ label : 'Roots', value : 'roots' },
{ label : 'Leaves', value : 'leaves' },
{ label : 'None', value : '' } ]
},
color_picker_nodes : {
label : 'Select a color for nodes',
type : 'color',
value : '#548DB8'
},
color_picker_edges : {
label : 'Select a color for edges',
type : 'color',
value : '#A5A5A5'
},
color_picker_highlighted : {
label : 'Select a color for highlighted nodes and edges',
type : 'color',
value : '#C00000'
}
}
}
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 31 */
/***/ function(module, exports, __webpack_require__) {
config/plugins/visualizations/charts/static/repository/build/registry.js.map
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config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
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@@ -1 +1 @@
define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), biojs_phylocanvas:require( "visualizations/biojs/phylocanvas/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_basic:require( "visualizations/cytoscape/basic/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );
define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), biojs_phylocanvas:require( "visualizations/biojs/phylocanvas/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_viewer:require( "visualizations/cytoscape/viewer/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );
config/plugins/visualizations/charts/static/repository/registry.json
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@@ -3,7 +3,7 @@
"jqplot" : [ "bar", "boxplot", "histogram_discrete", "line", "scatter" ],
"biojs" : [ "msa", "drawrnajs", "phylocanvas" ],
"others" : [ "example", "heatmap", "heatmap_cluster" ],
"cytoscape" : [ "basic" ],
"cytoscape" : [ "viewer" ],
"pv" : [ "viewer" ],
"benfred" : [ "venn" ],
"ngl" : [ "viewer" ]
config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
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@@ -0,0 +1,87 @@
/** Convert SIF files to JSON in a format required by Cytoscape
for rendering the graph */
/** Inspired from https://www.npmjs.com/package/sif.js */
define( [], function() {
function SIFJS() {};
// Private variables and methods
var nodes = {}, links = {}, content = [];
// Add a node
var _getNode = function( id ) {
if(!nodes[id]) {
nodes[id] = {id: id};
}
return nodes[id];
};
// Parse each line of the SIF file
var _parse = function( line, i ) {
var source = _getNode( line[0] ), interaction = ( line[1] ? line[1] : "" ), j, length;
line = ( line.split('\t').length > 1 ) ? line.split('\t') : line.split(' ');
if( line.length && line.length > 0 && line[0] !== "" ) {
if( interaction !== "" ) {
// Get all the target nodes for a source
for ( j = 2, length = line.length; j < length; j++ ) {
if( line[j] !== "" ) {
// Create an object for each target for the source
var target = _getNode( line[j] ),
relation_object = {target: target.id,
source: source.id,
id: source.id + target.id,
relation: interaction.replace(/[''""]+/g, '') }; // Replace quotes in relation
if( source < target ) {
links[ source.id + target.id + interaction ] = relation_object;
} else {
links[ target.id + source.id + interaction ] = relation_object;
}
}
}
}
// Handle the case of single node i.e. no relation with any other node
// and only the source exists
else {
links[ source.id ] = { target: "", source: source.id, id: source.id, relation: "" };
}
}
};
// Convert to array from objects
var _toArr = function( obj ) {
var arr = [];
for (var key in obj) {
arr.push( obj[key] );
}
return arr;
};
// Make content from list of nodes and links
var _toDataArr = function( nodes, links ) {
var content = [], node_length, links_length;
// Make a list of all nodes
for(var i = 0, node_length = nodes.length; i < node_length; i++) {
content.push( { 'data': nodes[i] } );
}
// Make a list of all relationships among nodes
for(var i = 0, links_length = links.length; i < links_length; i++) {
content.push( { 'data': links[i] } );
}
return content;
};
// Public method. Return graph data as JSON
SIFJS.parse = function( text ) {
var lines = text.split('\n'), i, length, nodesarr, linksarr;
for ( i = 0, length = lines.length; i < length; i++ ) {
_parse( lines[i], i );
}
nodesarr = _toArr( nodes );
linksarr = _toArr( links );
return { content: _toDataArr( nodesarr, linksarr ) };
};
return {
SIFJS : SIFJS
};
});
config/plugins/visualizations/charts/static/repository/utilities/utils.js
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@@ -120,4 +120,4 @@ define( [], function() {
clone : clone,
isJSON : isJSON
};
});
});
config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
-9
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@@ -1,9 +0,0 @@
define( [], function() {
return {
title : 'Cytoscape (Default)',
library : 'Cytoscape',
datatypes : [ 'json' ],
keywords : 'cytoscape graph nodes edges',
description : 'Basic Cytoscape viewer for connected graphs hosted at http://js.cytoscape.org.'
}
});
config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
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config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
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define( [ 'utilities/utils', 'plugins/cytoscape/cytoscape' ], function( Utils, Cytoscape ) {
return Backbone.Model.extend({
initialize: function( options ) {
var chart = options.chart;
var dataset = options.dataset;
Utils.get( {
url : dataset.download_url,
success : function( content ) {
try {
Cytoscape( Utils.merge( content, {
container: $( '#' + options.targets[ 0 ] ),
layout: {
name: 'cose',
idealEdgeLength: 100,
nodeOverlap: 20
},
style: Cytoscape.stylesheet()
.selector('node')
.css({
'content': 'data(name)',
'text-valign': 'center',
'color': 'white',
'text-outline-width': 2,
'text-outline-color': '#888'
})
.selector('edge')
.css({
'target-arrow-shape': 'triangle'
})
.selector(':selected')
.css({
'background-color': 'black',
'line-color': 'black',
'target-arrow-color': 'black',
'source-arrow-color': 'black'
})
.selector('.faded')
.css({
'opacity': 0.25,
'text-opacity': 0
})
} ) );
chart.state( 'ok', 'Chart drawn.' );
} catch( err ) {
chart.state( 'failed', err );
}
options.process.resolve();
},
error: function() {
chart.state( 'failed', 'Failed to access dataset.' );
options.process.resolve();
}
});
}
});
});
config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
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define( [], function() {
return {
title : 'Cytoscape',
library : 'Cytoscape',
datatypes : [ 'sif', 'json' ],
keywords : 'cytoscape graph nodes edges',
description : 'A viewer based on graph theory/ network library for analysis and visualisation hosted at http://js.cytoscape.org.',
settings : {
curve_style : {
label : 'Curve style',
help : 'Select a curving method used to separate two or more edges between two nodes.',
type : 'select',
display : 'radio',
value : 'haystack',
data : [ { label : 'Haystack', value : 'haystack' },
{ label : 'Bezier', value : 'bezier' },
{ label : 'Unbundled bezier', value : 'unbundled-bezier' },
{ label : 'Segments', value: 'segments' } ]
},
layout_name : {
label : 'Layout name',
help : 'Select a kind of position of nodes in graph.',
type : 'select',
display : 'radio',
value : 'haystack',
data : [ { label : 'Breadth First', value : 'breadthfirst' },
{ label : 'Circle', value : 'circle' },
{ label : 'Concentric', value : 'concentric' },
{ label : 'Cose', value : 'cose' },
{ label : 'Grid', value : 'grid' },
{ label : 'Null', value: 'null' },
{ label : 'Preset', value : 'preset' },
{ label : 'Random', value : 'random' } ]
},
directed : {
label : 'Directed/Undirected',
help : 'Select a kind of edge.',
type : 'select',
display : 'radio',
value : '',
data : [ { label : 'Directed', value : 'triangle' },
{ label : 'Undirected', value : '' } ]
},
search_algorithm : {
label : 'Graph algorithms',
help : 'Select a search algorithm. For Breadth First Search and Depth First Search, please click on any node of the graph. For A*, please click on two nodes, one for the root and another for the destination.',
type : 'select',
display : 'radio',
value : '',
data : [ { label : 'Breadth First Search', value : 'bfs' },
{ label : 'Depth First Search', value : 'dfs' },
{ label : 'Minimum Spanning Tree (Kruskal)', value : 'kruskal' },
{ label : 'A*', value : 'astar' },
{ label : 'None', value : '' } ]
},
graph_traversal: {
label : 'Graph traversal',
help : 'To select a graph traversal type, please click on any node of the graph',
type : 'select',
display : 'radio',
value : '',
data : [ { label : 'Successors', value : 'successors' },
{ label : 'Predecessors', value : 'predecessors' },
{ label : 'Outgoers', value : 'outgoers' },
{ label : 'Incomers', value : 'incomers' },
{ label : 'Roots', value : 'roots' },
{ label : 'Leaves', value : 'leaves' },
{ label : 'None', value : '' } ]
},
color_picker_nodes : {
label : 'Select a color for nodes',
type : 'color',
value : '#548DB8'
},
color_picker_edges : {
label : 'Select a color for edges',
type : 'color',
value : '#A5A5A5'
},
color_picker_highlighted : {
label : 'Select a color for highlighted nodes and edges',
type : 'color',
value : '#C00000'
}
}
}
});
config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
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config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
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define( [ 'utilities/utils', 'utilities/sifjson', 'plugins/cytoscape/cytoscape' ], function( Utils, SIF, Cytoscape ) {
return Backbone.Model.extend({
initialize: function( options ) {
var self = this,
chart = options.chart,
dataset = options.dataset,
settings = options.chart.settings,
data_content = null,
cytoscape = null,
astar_root = "",
astar_destination = "",
sif_file_ext = "sif",
highlighted_color = settings.get( 'color_picker_highlighted' );
Utils.get( {
url : dataset.download_url,
success : function( content ) {
// Select data for the graph
if( dataset.file_ext === sif_file_ext ) {
data_content = SIF.SIFJS.parse( content ).content;
}
else {
data_content = content.elements ? content.elements : content;
}
try {
cytoscape = Cytoscape({
container: document.getElementById( options.targets[ 0 ] ),
layout: {
name: settings.get( 'layout_name' ),
idealEdgeLength: 100,
nodeOverlap: 20
},
minZoom: 0.1,
maxZoom: 20,
style: [{
selector: 'node',
style: {
'background-color': settings.get( 'color_picker_nodes' ),
'opacity': 1,
'content': 'data(id)',
'text-valign': 'center',
}
},
{
selector: 'core',
style: {
'selection-box-color':'#AAD8FF',
'selection-box-border-color':'#8BB0D0',
'selection-box-opacity':'0.5'
}
},
{
selector: 'edge',
style: {
'curve-style': settings.get( 'curve_style' ),
'haystack-radius': 0,
'width': 3,
'opacity': 1,
'line-color': settings.get( 'color_picker_edges' ),
'target-arrow-shape': settings.get( 'directed' ),
"overlay-padding":"3px"
}
},
{
selector:'node:selected',
style: {
"border-width": "6px",
"border-color": "#AAD8FF",
"border-opacity": "0.5",
"background-color": "#77828C",
"text-outline-color": "#77828C"
}
},
{
selector: '.searchpath',
style: {
'background-color': highlighted_color,
'line-color': highlighted_color,
'target-arrow-color': highlighted_color,
'transition-property': 'background-color, line-color, target-arrow-color',
'transition-duration': '0.5s'
}
}],
elements: data_content // Set the JSON data for viewing
});
// Highlight the minimum spanning tree found using Kruskal algorithm
if( settings.get( 'search_algorithm' ) === "kruskal" ) {
var kruskal = cytoscape.elements().kruskal();
kruskal.edges().addClass( 'searchpath' );
}
// Register tap (clicking a node) event on graph nodes
// On tapping any node, BFS or DFS start from that node
cytoscape.$( 'node' ).on('tap', function( e ) {
var ele = e.cyTarget,
search_algorithm = settings.get( 'search_algorithm' ),
traversal_type = settings.get( 'graph_traversal' );
// If search algorithm and traversal both are chosen,
// search algorithm will take preference
if( settings.get( 'search_algorithm' ) !== "" ) {
self.run_search_algorithm( cytoscape, ele.id(), search_algorithm, self );
}
else if( settings.get( 'graph_traversal' ) !== "" ) {
self.run_traversal_type( cytoscape, ele.id(), traversal_type );
}
});
chart.state( 'ok', 'Chart drawn.' );
// Re-renders the graph view when window is resized
$( window ).resize( function() { cytoscape.layout(); } );
} catch( err ) {
chart.state( 'failed', err );
}
options.process.resolve();
},
error: function() {
chart.state( 'failed', 'Failed to access dataset.' );
options.process.resolve();
}
});
},
run_search_algorithm: function( cytoscape, root_id, type, self ) {
var algorithm = "", i = 0;
var selectNextElement = function() {
if( i < algorithm.path.length ) {
// Add css class for the selected edge(s)
algorithm.path[i].addClass( 'searchpath' );
i++;
// Animate the edges and nodes coloring
// of the path with a delay of 500ms
setTimeout( selectNextElement, 500 );
}
};
switch( type ) {
// Breadth First Search
case "bfs":
algorithm = cytoscape.elements().bfs( '#' + root_id, function() { }, true );
selectNextElement();
break;
// Depth First Search
case "dfs":
algorithm = cytoscape.elements().dfs( '#' + root_id, function() { }, true );
selectNextElement();
break;
// A* search
case "astar":
// Choose root and destination for performing A*
if( !self.astar_root ) {
self.astar_root = root_id;
}
else {
self.astar_destination = root_id;
}
if( self.astar_root && self.astar_destination ) {
algorithm = cytoscape.elements().aStar({ root: "#" + self.astar_root, goal: "#" + self.astar_destination },function() {}, true);
selectNextElement();
}
default:
return;
}
},
run_traversal_type: function( cytoscape, root_id, type ) {
var node_collection;
switch( type ) {
// Recursively get edges (and their sources) coming into the nodes in a collection
case "predecessors":
node_collection = cytoscape.$( '#' + root_id ).predecessors();
break;
// Recursively get edges (and their targets) coming out of the nodes in a collection
case "successors":
node_collection = cytoscape.$( '#' + root_id ).successors();
break;
// Get edges (and their targets) coming out of the nodes in a collection.
case "outgoers":
node_collection = cytoscape.$( '#' + root_id ).outgoers();
break;
// Get edges (and their sources) coming into the nodes in a collection.
case "incomers":
node_collection = cytoscape.$( '#' + root_id ).incomers();
break;
// From the set of calling nodes, get the nodes which are roots
case "roots":
node_collection = cytoscape.$( '#' + root_id ).roots();
break;
// From the set of calling nodes, get the nodes which are leaves
case "leaves":
node_collection = cytoscape.$( '#' + root_id ).leaves();
break;
default:
return;
}
// Add CSS class for selected nodes and edges
node_collection.edges().addClass( 'searchpath' );
node_collection.nodes().addClass( 'searchpath' );
}
});
});
display_applications/igv/bigwig.xml
+1 -1
View File
@@ -2,7 +2,7 @@
<display id="igv_bigwig" version="1.0.0" name="display with IGV">
<!-- Load links from file: one line to one link -->
<dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
<dynamic_links site_type="igv" skip_startswith="#" id="0" name="1">
<!-- Define parameters by column from file, allow splitting on builds -->
<dynamic_param name="site_id" value="0"/>
doc/source/admin/framework_dependencies.rst
+49 -49
View File
@@ -1,7 +1,7 @@
.. _framework-dependencies:
Galaxy Framework Dependencies
=============================
Framework Dependencies
======================
Galaxy is a large Python application with a long list of `Python module
dependencies`_. As a result, the Galaxy developers have made significant effort
@@ -84,7 +84,7 @@ live in ``/srv/galaxy/venv`` and the Galaxy source code has been cloned to
``/srv/galaxy/server``.
.. code-block:: console
$ virtualenv /srv/galaxy/venv
New python executable in /srv/galaxy/venv/bin/python
Installing setuptools, pip, wheel...done.
@@ -100,12 +100,12 @@ yourself to set up Galaxy pip and the dependencies without creating a
virtualenv using the ``--no-create-venv`` option:
.. code-block:: console
(venv)$ PYTHONPATH= sh /srv/galaxy/server/scripts/common_startup.sh --no-create-venv
Ignoring indexes: https://pypi.python.org/simple
Collecting pip
Downloading https://wheels.galaxyproject.org/packages/pip-8.0.0+gx1-py2.py3-none-any.whl (1.2MB)
100% |████████████████████████████████| 1.2MB 37.8MB/s
100% |████████████████████████████████| 1.2MB 37.8MB/s
Installing collected packages: pip
Found existing installation: pip 7.1.2
Uninstalling pip-7.1.2:
@@ -113,13 +113,13 @@ virtualenv using the ``--no-create-venv`` option:
Successfully installed pip-8.0.0+gx1
Collecting bx-python==0.7.3 (from -r requirements.txt (line 2))
Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-linux_x86_64.whl (1.7MB)
100% |████████████████████████████████| 1.7MB 25.4MB/s
100% |████████████████████████████████| 1.7MB 25.4MB/s
...
Collecting pysam==0.8.3+gx1 (from -r requirements.txt (line 69))
Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.3+gx1-cp27-cp27mu-linux_x86_64.whl (7.4MB)
100% |████████████████████████████████| 7.4MB 15.1MB/s
100% |████████████████████████████████| 7.4MB 15.1MB/s
Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy,
mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype,
repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker,
@@ -307,48 +307,48 @@ automatic fetching of pinned dependencies.
The following NEW packages will be INSTALLED:
babel: 2.1.1-py27_0
bioblend: 0.7.0-py27_0
boto: 2.38.0-py27_0
babel: 2.1.1-py27_0
bioblend: 0.7.0-py27_0
boto: 2.38.0-py27_0
bx-python: 0.7.3-np110py27_1
cheetah: 2.4.4-py27_0
decorator: 4.0.6-py27_0
docutils: 0.12-py27_0
ecdsa: 0.11-py27_0
fabric: 1.10.2-py27_0
libgfortran: 1.0-0
mako: 1.0.3-py27_0
markupsafe: 0.23-py27_0
mercurial: 3.4.2-py27_0
nose: 1.3.7-py27_0
numpy: 1.10.2-py27_0
openblas: 0.2.14-3
openssl: 1.0.2e-0
paramiko: 1.15.2-py27_0
paste: 1.7.5.1-py27_0
pastedeploy: 1.5.2-py27_1
pip: 7.1.2-py27_0
pycrypto: 2.6.1-py27_0
python: 2.7.11-0
pytz: 2015.7-py27_0
pyyaml: 3.11-py27_1
readline: 6.2-2
repoze.lru: 0.6-py27_0
requests: 2.9.1-py27_0
requests-toolbelt: 0.5.0-py27_0
routes: 2.2-py27_0
setuptools: 19.2-py27_0
six: 1.10.0-py27_0
sqlalchemy: 1.0.11-py27_0
sqlite: 3.9.2-0
sqlparse: 0.1.18-py27_0
tk: 8.5.18-0
webob: 1.4.1-py27_0
wheel: 0.26.0-py27_1
yaml: 0.1.6-0
zlib: 1.2.8-0
cheetah: 2.4.4-py27_0
decorator: 4.0.6-py27_0
docutils: 0.12-py27_0
ecdsa: 0.11-py27_0
fabric: 1.10.2-py27_0
libgfortran: 1.0-0
mako: 1.0.3-py27_0
markupsafe: 0.23-py27_0
mercurial: 3.4.2-py27_0
nose: 1.3.7-py27_0
numpy: 1.10.2-py27_0
openblas: 0.2.14-3
openssl: 1.0.2e-0
paramiko: 1.15.2-py27_0
paste: 1.7.5.1-py27_0
pastedeploy: 1.5.2-py27_1
pip: 7.1.2-py27_0
pycrypto: 2.6.1-py27_0
python: 2.7.11-0
pytz: 2015.7-py27_0
pyyaml: 3.11-py27_1
readline: 6.2-2
repoze.lru: 0.6-py27_0
requests: 2.9.1-py27_0
requests-toolbelt: 0.5.0-py27_0
routes: 2.2-py27_0
setuptools: 19.2-py27_0
six: 1.10.0-py27_0
sqlalchemy: 1.0.11-py27_0
sqlite: 3.9.2-0
sqlparse: 0.1.18-py27_0
tk: 8.5.18-0
webob: 1.4.1-py27_0
wheel: 0.26.0-py27_1
yaml: 0.1.6-0
zlib: 1.2.8-0
Proceed ([y]/n)?
Proceed ([y]/n)?
Fetching packages ...
boto-2.38.0-py 100% |############################################| Time: 0:00:00 3.27 MB/s
@@ -397,7 +397,7 @@ automatic fetching of pinned dependencies.
Collecting WebHelpers (from -r lib/galaxy/dependencies/requirements.txt (line 15))
Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB)
100% |████████████████████████████████| 151kB 55.7MB/s
100% |████████████████████████████████| 151kB 55.7MB/s
...
@@ -425,7 +425,7 @@ install uWSGI into Galaxy virtualenv (by default, ``.venv``) using pip, e.g.:
(.venv)$ pip install uwsgi
Collecting uwsgi
Downloading uwsgi-2.0.12.tar.gz (784kB)
100% |████████████████████████████████| 786kB 981kB/s
100% |████████████████████████████████| 786kB 981kB/s
Building wheels for collected packages: uwsgi
Running setup.py bdist_wheel for uwsgi
Stored in directory: /home/nate/.cache/pip/wheels/a4/7b/7c/8cbe2fe2c2b963173361cc18aa726f165dc4803effbb8195fc
doc/source/admin/index.rst
+1
View File
@@ -11,4 +11,5 @@ This documentation is in the midst of being ported and unified based on resource
dependency_resolvers
conda_faq
framework_dependencies
reports
useful_scripts
doc/source/admin/reports.md
+21
View File
@@ -0,0 +1,21 @@
# Galaxy Reports
Galaxy includes a report tool that is separate from the main process but which gives lots of potentially useful information about the usage of a Galaxy instance, for example the numbers of jobs that have been run each month, how much disk space each user is currently consuming and so on.
## Setup on localhost
The report tool takes its configuration settings from a file called reports.ini, which is located in the config subdirectory of the Galaxy distribution.
Configuring the reports for your local setup is a case of:
* Making a copy of `reports.ini.sample` called `reports.ini`.
* Editing the `database_connection` parameter to match the one in your `galaxy.ini` file
* Optionally, editing the `port` parameter (by default the tool uses port 9001)
You should also set the 'salt' parameter `session_secret` if you intend to expose the reports via the web proxy (see below).
Then you can start the report server using `sh run_reports.sh` and view the reports by pointing a web browser running on the same server to http://127.0.0.1:9001. If you'd like the report tool to persist between sessions then use `sh run_reports.sh --daemon` to run it as a background process. As with Galaxy itself, use `--stop-daemon` to halt the background process. (The log file is written to `reports_webapp.log` if you need to try and debug a problem.)
## Expose Outside
To make your reports available from outside of the localhost using NGINX proxy server you can check out the [blogpost](http://galacticengineer.blogspot.co.uk/2015/06/exposing-galaxy-reports-via-nginx-in.html) by Peter Briggs.
doc/source/admin/useful_scripts.rst
+2 -2
View File
@@ -1,5 +1,5 @@
Useful Scripts and Administration Tricks
========================================
Scripts & Tricks
================
This page aims to help ease the burden of administration with some easy to use scripts and documentation on what is available for admins to use.
doc/source/api/api.rst
+209
View File
@@ -0,0 +1,209 @@
Galaxy API
==========
annotations
-----------
.. automodule:: galaxy.webapps.galaxy.api.annotations
authenticate
------------
.. automodule:: galaxy.webapps.galaxy.api.authenticate
configuration
-------------
.. automodule:: galaxy.webapps.galaxy.api.configuration
dataset_collections
-------------------
.. automodule:: galaxy.webapps.galaxy.api.dataset_collections
datasets
--------
.. automodule:: galaxy.webapps.galaxy.api.datasets
datatypes
---------
.. automodule:: galaxy.webapps.galaxy.api.datatypes
extended_metadata
-----------------
.. automodule:: galaxy.webapps.galaxy.api.extended_metadata
folder_contents
---------------
.. automodule:: galaxy.webapps.galaxy.api.folder_contents
folders
-------
.. automodule:: galaxy.webapps.galaxy.api.folders
forms
-----
.. automodule:: galaxy.webapps.galaxy.api.forms
genomes
-------
.. automodule:: galaxy.webapps.galaxy.api.genomes
group_roles
-----------
.. automodule:: galaxy.webapps.galaxy.api.group_roles
group_users
-----------
.. automodule:: galaxy.webapps.galaxy.api.group_users
groups
------
.. automodule:: galaxy.webapps.galaxy.api.groups
histories
---------
.. automodule:: galaxy.webapps.galaxy.api.histories
history_contents
----------------
.. automodule:: galaxy.webapps.galaxy.api.history_contents
item_tags
---------
.. automodule:: galaxy.webapps.galaxy.api.item_tags
job_files
---------
.. automodule:: galaxy.webapps.galaxy.api.job_files
jobs
----
.. automodule:: galaxy.webapps.galaxy.api.jobs
lda_datasets
------------
.. automodule:: galaxy.webapps.galaxy.api.lda_datasets
libraries
---------
.. automodule:: galaxy.webapps.galaxy.api.libraries
library_contents
----------------
.. automodule:: galaxy.webapps.galaxy.api.library_contents
metrics
-------
.. automodule:: galaxy.webapps.galaxy.api.metrics
page_revisions
--------------
.. automodule:: galaxy.webapps.galaxy.api.page_revisions
pages
-----
.. automodule:: galaxy.webapps.galaxy.api.pages
provenance
----------
.. automodule:: galaxy.webapps.galaxy.api.provenance
quotas
------
.. automodule:: galaxy.webapps.galaxy.api.quotas
remote_files
------------
.. automodule:: galaxy.webapps.galaxy.api.remote_files
request_types
-------------
.. automodule:: galaxy.webapps.galaxy.api.request_types
requests
--------
.. automodule:: galaxy.webapps.galaxy.api.requests
roles
-----
.. automodule:: galaxy.webapps.galaxy.api.roles
samples
-------
.. automodule:: galaxy.webapps.galaxy.api.samples
search
------
.. automodule:: galaxy.webapps.galaxy.api.search
tool_data
---------
.. automodule:: galaxy.webapps.galaxy.api.tool_data
tool_shed_repositories
----------------------
.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories
tools
-----
.. automodule:: galaxy.webapps.galaxy.api.tools
tours
-----
.. automodule:: galaxy.webapps.galaxy.api.tours
users
-----
.. automodule:: galaxy.webapps.galaxy.api.users
visualizations
--------------
.. automodule:: galaxy.webapps.galaxy.api.visualizations
webhooks
--------------
.. automodule:: galaxy.webapps.galaxy.api.webhooks
workflows
---------
.. automodule:: galaxy.webapps.galaxy.api.workflows
doc/source/api/ts_api.rst
+44
View File
@@ -0,0 +1,44 @@
Tool Shed API
=============
authenticate
------------
.. automodule:: galaxy.webapps.tool_shed.api.authenticate
categories
----------
.. automodule:: galaxy.webapps.tool_shed.api.categories
configuration
-------------
.. automodule:: galaxy.webapps.tool_shed.api.configuration
groups
------
.. automodule:: galaxy.webapps.tool_shed.api.groups
repositories
------------
.. automodule:: galaxy.webapps.tool_shed.api.repositories
repository_revisions
--------------------
.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions
tools
-----
.. automodule:: galaxy.webapps.tool_shed.api.tools
users
-----
.. automodule:: galaxy.webapps.tool_shed.api.users
doc/source/api_doc.rst
+9 -4
View File
@@ -18,12 +18,17 @@ The Galaxy API addresses these and other situations by exposing Galaxy
internals through an additional interface, known as an Application Programming
Interface, or API.
Various language specific bindings for interfacing with the Galaxy API have been developed by the Galaxy community including `Python <http://bioblend.readthedocs.io/en/latest/>`__, `PHP <https://github.com/galaxyproject/blend4php>`__, `Java <https://github.com/jmchilton/blend4j>`__, and `JavaScript <https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc>`__.
Overview of available API resources is available at https://galaxyproject.org/develop/api/.
.. toctree::
:maxdepth: 3
:maxdepth: 2
Galaxy API Quickstart <api/quickstart>
Quickstart <api/quickstart>
Galaxy API Guidelines <api/guidelines>
Development Guidelines <api/guidelines>
Documentation <api/api>
Galaxy API Documentation <lib/galaxy.webapps.galaxy.api>
doc/source/conf.py
+3 -1
View File
@@ -46,8 +46,10 @@ extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sp
templates_path = ['_templates']
# Configure default autodoc's action
autodoc_default_flags = [ 'members', 'undoc-members', 'show-inheritance' ]
autodoc_default_flags = [ 'members', 'undoc-members' ]
# Prevent alphabetical reordering of module members.
autodoc_member_order = 'bysource'
def dont_skip_init(app, what, name, obj, skip, options):
if name == "__init__":
doc/source/index.rst
+4 -5
View File
@@ -31,7 +31,7 @@ For more information on the Galaxy Project, please visit the https://galaxyproje
.. _dev-docs:
.. toctree::
:maxdepth: 1
:maxdepth: 2
:caption: Developer Documentation
Development <dev/index>
@@ -53,15 +53,14 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
Building this Documentation
===========================
If you have your own copy of the Galaxy source code, you can also generate your own version of this documentation:
If you have your own copy of the Galaxy source code, you can also generate your own version of this documentation. Run the following command from the Galaxy's root:
::
$ make -C doc/ html
$ make docs
The generated documentation will be in ``doc/build/html/`` and can be viewed with a web browser. Note that you will need to install Sphinx and a fair number of module dependencies before this will produce output.
The generated documentation will be in ``doc/build/html/`` and can be viewed with a web browser. Note that you will need to install Sphinx and a other module dependencies which are listed in the Makefile in the Galaxy root folder.
doc/source/lib/galaxy.webapps.galaxy.api.rst
-324
View File
@@ -1,324 +0,0 @@
galaxy.webapps.galaxy.api package
=================================
.. automodule:: galaxy.webapps.galaxy.api
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.webapps.galaxy.api.annotations module
--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.annotations
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.authenticate module
---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.authenticate
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.configuration module
----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.configuration
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.dataset_collections module
----------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.dataset_collections
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.datasets module
-----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.datasets
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.datatypes module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.datatypes
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.extended_metadata module
--------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.extended_metadata
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.folder_contents module
------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.folder_contents
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.folders module
----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.folders
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.forms module
--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.forms
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.genomes module
----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.genomes
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.group_roles module
--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.group_roles
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.group_users module
--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.group_users
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.groups module
---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.groups
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.histories module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.histories
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.history_contents module
-------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.history_contents
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.item_tags module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.item_tags
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.job_files module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.job_files
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.jobs module
-------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.jobs
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.lda_datasets module
---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.lda_datasets
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.libraries module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.libraries
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.library_contents module
-------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.library_contents
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.metrics module
----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.metrics
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.page_revisions module
-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.page_revisions
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.pages module
--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.pages
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.provenance module
-------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.provenance
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.quotas module
---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.quotas
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.remote_files module
---------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.remote_files
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.request_types module
----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.request_types
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.requests module
-----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.requests
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.roles module
--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.roles
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.samples module
----------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.samples
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.search module
---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.search
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.tool_data module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.tool_data
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.tool_shed_repositories module
-------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.tools module
--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.tools
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.users module
--------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.users
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.visualizations module
-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.visualizations
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.workflows module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.workflows
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.webapps.tool_shed.api.rst
-76
View File
@@ -1,76 +0,0 @@
galaxy.webapps.tool_shed.api package
====================================
.. automodule:: galaxy.webapps.tool_shed.api
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.webapps.tool_shed.api.authenticate module
------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.authenticate
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.categories module
----------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.categories
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.configuration module
-------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.configuration
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.groups module
------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.groups
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.repositories module
------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.repositories
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.repository_revisions module
--------------------------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.tools module
-----------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.tools
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.tool_shed.api.users module
-----------------------------------------
.. automodule:: galaxy.webapps.tool_shed.api.users
:members:
:undoc-members:
:show-inheritance:
doc/source/releases/_header.rst
+2 -2
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@@ -1,3 +1,3 @@
.. image:: https://wiki.galaxyproject.org/Images/GalaxyLogos?action=AttachFile&do=get&target=galaxy_logo_25percent_transparent.png
:alt: Get the Galaxy Release Your Way
.. image:: https://galaxyproject.org/images/galaxy-logos/galaxy_logo_25percent_transparent.png
:alt: Get Galaxy
:target: http://getgalaxy.org
doc/source/ts_api_doc.rst
+3 -3
View File
@@ -3,7 +3,7 @@ Tool Shed API Documentation
The Galaxy Tool Shed can be accessed programmatically using API described
here via shell scripts and other programs.
To interact with the API you first need to log in as your user, navigate
To interact with the API you first need to obtain API key e.g.: log in as your user, navigate
to the API Keys page in the User menu, and generate a new API key. This
key you have to attach to every request as a parameter. Example:
@@ -12,6 +12,6 @@ key you have to attach to every request as a parameter. Example:
GET https://toolshed.g2.bx.psu.edu/api/repositories?q=fastq?key=SOME_KEY_HERE
.. toctree::
:maxdepth: 3
:maxdepth: 2
Toolshed API Documentation <lib/galaxy.webapps.tool_shed.api>
API Documentation <api/ts_api>
lib/galaxy/tools/__init__.py
+1
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@@ -128,6 +128,7 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
# Converters
"CONVERTER_bed_to_fli_0",
"CONVERTER_fastq_to_fqtoc0",
"CONVERTER_gff_to_fli_0",
"CONVERTER_gff_to_interval_index_0",
"CONVERTER_maf_to_fasta_0",
"CONVERTER_maf_to_interval_0",