galaxy-commits July 2012

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commit/galaxy-central: jgoecks: Small viz tweaks.
by Bitbucket 11 Jul '12

11 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a2d161919806/ changeset: a2d161919806 user: jgoecks date: 2012-07-11 19:19:23 summary: Small viz tweaks. affected #: 3 files diff -r 33676ce91213156e434e9c9c2f2def8d9fbbecc2 -r a2d1619198063084b99a1e6e8c75e1658593c448 static/scripts/packed/viz/paramamonster.js --- a/static/scripts/packed/viz/paramamonster.js +++ b/static/scripts/packed/viz/paramamonster.js @@ -1,1 +1,1 @@ -var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var ParamaMonsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:ParamaMonsterTrack});var ParamaMonsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"ParamaMonsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"paramamonster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var ParamaMonsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()},tipsy_config:{gravity:"s"}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".tipsy").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");if(!a){return}$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i=b.model.get("mode");$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{tipsy_config:{gravity:"s"}});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1],m=$("#center").position().left;h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+m))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+20).append("g").attr("transform","translate(40, 10)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var ParamaMonsterVisualizationView=Backbone.View.extend({className:"paramamonster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a})},render:function(){var g=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(g.$el);var j=this,d=j.model.get("regions"),h=$("<tr/>").appendTo(this.track_collection_container);d.each(function(k){h.append($("<th>").text(k.toString()))});h.children().first().attr("colspan",2);var e=$("<div>").addClass("tiles");$("#right").append(e.append(this.track_collection_container));j.model.get("tracks").each(function(k){j.add_track(k)});var i=$(this.helpText).addClass("help"),f=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tipsy").remove();i.remove()},tipsy_config:{gravity:"s"}}]);i.prepend(f.$el.css("float","right"));$("#center").append(i);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var c=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tipsy_config:{gravity:"n"}});var b=["Squish","Pack"],a={};_.each(b,function(k){a[k]=function(){j.model.set("default_mode",k);j.model.get("tracks").each(function(l){l.set("mode",k)})}});make_popupmenu(c.$el.find(".chevron-expand"),a);c.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(c.$el)},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new ParamaMonsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new ParamaMonsterTrack({settings:m,regions:d,mode:a.model.get("default_mode")});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);n.set("track",o)})},m*10000)})})})}}); \ No newline at end of file +var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var ParamaMonsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:ParamaMonsterTrack});var ParamaMonsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"ParamaMonsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"paramamonster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var ParamaMonsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()},tipsy_config:{gravity:"s"}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".tipsy").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");if(!a){return}$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i=b.model.get("mode");$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{tipsy_config:{gravity:"s"}});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1],m=$("#center").position().left;h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+m))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var ParamaMonsterVisualizationView=Backbone.View.extend({className:"paramamonster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a})},render:function(){var g=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(g.$el);var j=this,d=j.model.get("regions"),h=$("<tr/>").appendTo(this.track_collection_container);d.each(function(k){h.append($("<th>").text(k.toString()))});h.children().first().attr("colspan",2);var e=$("<div>").addClass("tiles");$("#right").append(e.append(this.track_collection_container));j.model.get("tracks").each(function(k){j.add_track(k)});var i=$(this.helpText).addClass("help"),f=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tipsy").remove();i.remove()},tipsy_config:{gravity:"s"}}]);i.prepend(f.$el.css("float","right"));$("#center").append(i);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var c=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tipsy_config:{gravity:"n"}});var b=["Squish","Pack"],a={};_.each(b,function(k){a[k]=function(){j.model.set("default_mode",k);j.model.get("tracks").each(function(l){l.set("mode",k)})}});make_popupmenu(c.$el.find(".chevron-expand"),a);c.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(c.$el)},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new ParamaMonsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new ParamaMonsterTrack({settings:m,regions:d,mode:a.model.get("default_mode")});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);n.set("track",o)})},m*10000)})})})}}); \ No newline at end of file diff -r 33676ce91213156e434e9c9c2f2def8d9fbbecc2 -r a2d1619198063084b99a1e6e8c75e1658593c448 static/scripts/viz/paramamonster.js --- a/static/scripts/viz/paramamonster.js +++ b/static/scripts/viz/paramamonster.js @@ -638,9 +638,9 @@ var vis = d3.select(this.$el[0]) .append("svg") .attr("width", this.width) - .attr("height", this.height + 20) + .attr("height", this.height + 30) .append("g") - .attr("transform", "translate(40, 10)"); + .attr("transform", "translate(40, 20)"); // Draw links. var link = vis.selectAll("path.link") diff -r 33676ce91213156e434e9c9c2f2def8d9fbbecc2 -r a2d1619198063084b99a1e6e8c75e1658593c448 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -57,7 +57,6 @@ } } ]); - menu.render(); menu.$el.attr("style", "float: right"); $("#center .unified-panel-header-inner").append(menu.$el); // Manual tipsy config because default gravity is S and cannot be changed. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for history items going to different histories if current history is switched while the workflow is still being queued.
by Bitbucket 11 Jul '12

11 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/33676ce91213/ changeset: 33676ce91213 user: dan date: 2012-07-11 18:01:16 summary: Fix for history items going to different histories if current history is switched while the workflow is still being queued. affected #: 1 file diff -r f673cb8e75d9978ef069fd0dcad9ee0dc065ac6e -r 33676ce91213156e434e9c9c2f2def8d9fbbecc2 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1409,6 +1409,9 @@ nh_name = '%s on %s' % (nh_name, mx_ds_name) new_history = trans.app.model.History( user=trans.user, name=nh_name ) trans.sa_session.add( new_history ) + target_history = new_history + else: + target_history = trans.get_history() # Run each step, connecting outputs to inputs workflow_invocation = model.WorkflowInvocation() workflow_invocation.workflow = workflow @@ -1429,7 +1432,7 @@ except KeyError, k: error( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=new_history) + job, out_data = tool.execute( trans, step.state.inputs, history=target_history) outputs[ step.id ] = out_data # Create new PJA associations with the created job, to be run on completion. # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for installing tool dependencies, and uninstalling repositories and tool dependencies.
by Bitbucket 11 Jul '12

11 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f673cb8e75d9/ changeset: f673cb8e75d9 user: greg date: 2012-07-11 17:53:22 summary: Fixes for installing tool dependencies, and uninstalling repositories and tool dependencies. affected #: 2 files diff -r 005f732eb00f76e7d1319dfb8288953aff9b8939 -r f673cb8e75d9978ef069fd0dcad9ee0dc065ac6e lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1210,6 +1210,8 @@ ElementInclude.include( root ) fabric_version_checked = False for elem in root: + # Only install the package if it is not already installed. + can_install = False if elem.tag == 'package': package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) @@ -1217,8 +1219,6 @@ # The value of tool_dependencies will be None only when this method is called by the InstallManager. In that case, tool # dependency installation is not ajaxian, so the ToolDependency objects do not yet exist. if tool_dependencies: - # Only install the package if it is not already installed. - can_install = False for tool_dependency in tool_dependencies: if tool_dependency.name==package_name and tool_dependency.version==package_version: can_install = tool_dependency.status in [ app.model.ToolDependency.installation_status.NEVER_INSTALLED, @@ -1457,6 +1457,7 @@ log.debug( error_message ) if removed: tool_dependency.status = trans.model.ToolDependency.installation_status.UNINSTALLED + tool_dependency.error_message = None trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message diff -r 005f732eb00f76e7d1319dfb8288953aff9b8939 -r f673cb8e75d9978ef069fd0dcad9ee0dc065ac6e lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -437,6 +437,7 @@ tool_shed_repository.deleted = True if remove_from_disk_checked: tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.UNINSTALLED + tool_shed_repository.error_message = None else: tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.DEACTIVATED trans.sa_session.add( tool_shed_repository ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix the sqlite db connection string in the community app so local tool sheds will work when using sqlite.
by Bitbucket 11 Jul '12

11 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/005f732eb00f/ changeset: 005f732eb00f user: greg date: 2012-07-11 16:47:51 summary: Fix the sqlite db connection string in the community app so local tool sheds will work when using sqlite. affected #: 1 file diff -r 85dccacdfa80ba7818979049810a7891102fe2ef -r 005f732eb00f76e7d1319dfb8288953aff9b8939 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -17,13 +17,12 @@ config.configure_logging( self.config ) # Set up datatypes registry self.datatypes_registry = galaxy.datatypes.registry.Registry() - # TODO: Handle datatypes included in repositories - the following will only load datatypes_conf.xml. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection else: - db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Initialize database / check for appropriate schema version from galaxy.webapps.community.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, self.config.database_engine_options ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed.
by Bitbucket 10 Jul '12

10 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/85dccacdfa80/ changeset: 85dccacdfa80 user: dan date: 2012-07-10 23:35:30 summary: Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed. affected #: 2 files diff -r af62b5d831de40a19da96e8c1c4e20c02aa1983c -r 85dccacdfa80ba7818979049810a7891102fe2ef tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -208,7 +208,6 @@ <tool file="phenotype_association/lps.xml" /><tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /> - <tool file="variant_detection/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /><tool file="phenotype_association/dividePgSnpAlleles.xml" /> @@ -319,9 +318,6 @@ <tool file="indels/indel_sam2interval.xml" /><tool file="indels/indel_analysis.xml" /></section> - <section name="NGS: Variant Detection" id="variant_detection"> - <tool file="variant_detection/freebayes.xml" /> - </section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> diff -r af62b5d831de40a19da96e8c1c4e20c02aa1983c -r 85dccacdfa80ba7818979049810a7891102fe2ef tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -477,7 +477,6 @@ <tool file="phenotype_association/lps.xml" /><tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /> - <tool file="variant_detection/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /><tool file="phenotype_association/dividePgSnpAlleles.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 10 Jul '12

10 Jul '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6a75ab8e6a2b/ changeset: 6a75ab8e6a2b user: rmarenco date: 2012-07-10 23:20:57 summary: Fix dataset tool parameter information form. Fixes #773 affected #: 1 file diff -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b -r 6a75ab8e6a2bcc08b2a4ad8af55c4afe62e390de templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -19,19 +19,27 @@ %elif input.type == "conditional": <% current_case = param_values[input.name]['__current_case__'] %><tr> - <td>${input.label}</td> - <td>${current_case}</td> + ${ inputs_recursive_indent( text=input.test_param.label,depth=depth )} +  + <td>${input.cases[current_case].value}</td></tr> ${ inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth+1) } %elif getattr(input, "label", None): <tr> - <td>${input.label}</td> + ${inputs_recursive_indent( text=input.label,depth=depth )} <td>${input.value_to_display_text(param_values[input.name], trans.app)}</td></tr> %endif %endfor </%def> + ## function to add a indentation depending on the depth in a <tr> +<%def name="inputs_recursive_indent( text, depth )"> + <td style="padding-left: ${ ( depth - 1 ) * 10 }px"> + ${text} + </td> +</%def> + <table class="tabletip"><thead><tr><th colspan="2" style="font-size: 120%;"> https://bitbucket.org/galaxy/galaxy-central/changeset/af62b5d831de/ changeset: af62b5d831de user: rmarenco date: 2012-07-10 23:23:56 summary: Automerge affected #: 2 files diff -r 6a75ab8e6a2bcc08b2a4ad8af55c4afe62e390de -r af62b5d831de40a19da96e8c1c4e20c02aa1983c tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -314,9 +314,6 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Variant Detection" id="variant_detection"> - <tool file="variant_detection/freebayes.xml" /> - </section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> diff -r 6a75ab8e6a2bcc08b2a4ad8af55c4afe62e390de -r af62b5d831de40a19da96e8c1c4e20c02aa1983c tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -419,9 +419,6 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Variant Detection" id="variant_detection"> - <tool file="variant_detection/freebayes.xml" /> - </section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed.
by Bitbucket 10 Jul '12

10 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/791d67a5f3f3/ changeset: 791d67a5f3f3 user: dan date: 2012-07-10 23:20:55 summary: Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed. affected #: 2 files diff -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b -r 791d67a5f3f3c5f3c0bc51c9fe8df040a0407990 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -314,9 +314,6 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Variant Detection" id="variant_detection"> - <tool file="variant_detection/freebayes.xml" /> - </section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> diff -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b -r 791d67a5f3f3c5f3c0bc51c9fe8df040a0407990 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -419,9 +419,6 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Variant Detection" id="variant_detection"> - <tool file="variant_detection/freebayes.xml" /> - </section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Migrate the freebayes tool out of the Galaxy code distribution.
by Bitbucket 10 Jul '12

10 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3e6ab1cf0c2e/ changeset: 3e6ab1cf0c2e user: greg date: 2012-07-10 22:23:34 summary: Migrate the freebayes tool out of the Galaxy code distribution. affected #: 4 files diff -r d07c00d96b60746a1e83713530a9070bf818e16c -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b lib/galaxy/tool_shed/migrate/versions/0003_tools.py --- /dev/null +++ b/lib/galaxy/tool_shed/migrate/versions/0003_tools.py @@ -0,0 +1,12 @@ +""" +The freebayes tool has been eliminated from the distribution . The repository named freebayes from the main +Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance at the +location discussed above by running the following command. +""" + +import sys + +def upgrade(): + print __doc__ +def downgrade(): + pass diff -r d07c00d96b60746a1e83713530a9070bf818e16c -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b scripts/migrate_tools/0003_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0003_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml $@ diff -r d07c00d96b60746a1e83713530a9070bf818e16c -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b scripts/migrate_tools/0003_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0003_tools.xml @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="046c7983e2ff"> + <tool id="freebayes" version="0.0.2 " file="freebayes.xml" /> + </repository> +</toolshed> diff -r d07c00d96b60746a1e83713530a9070bf818e16c -r 3e6ab1cf0c2eebbc886a7911e970f43bbfde522b tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ /dev/null @@ -1,670 +0,0 @@ -<?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.2"> - <requirements> - <requirement type="package" version="0.9.4">freebayes</requirement> - <requirement type="package">samtools</requirement> - </requirements> - <description> - Bayesian genetic variant detector</description> - <command> - ##set up input files - #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): - ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && - ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && - #end for - ##finished setting up inputs - - ##start FreeBayes commandline - freebayes - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): - --bam "localbam_${bam_count}.bam" - #end for - --fasta-reference "${reference_fasta_filename}" - - ##outputs - --vcf "${output_vcf}" - - ##advanced options - #if str( $options_type.options_type_selector ) == "advanced": - ##additional outputs - #if $options_type.output_trace_option: - --trace "${output_trace}" - #end if - #if $options_type.output_failed_alleles_option: - --failed-alleles "${output_failed_alleles_bed}" - #end if - - ##additional inputs - #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": - --targets "${options_type.target_limit_type.input_target_bed}" - #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region": - --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}" - #end if - #if $options_type.input_sample_file: - --samples "${options_type.input_sample_file}" - #end if - #if $options_type.input_populations_file: - --populations "${options_type.input_populations_file}" - #end if - #if $options_type.input_cnv_map_bed: - --cnv-map "${options_type.input_cnv_map_bed}" - #end if - #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf": - --variant-input "${options_type.input_variant_type.input_variant_vcf}" - ${options_type.input_variant_type.only_use_input_alleles} - #end if - - ##reporting - #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set": - --pvar "${options_type.section_reporting_type.pvar}" - ${options_type.section_reporting_type.show_reference_repeats} - #end if - - ##population model - #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set": - --theta "${options_type.section_population_model_type.theta}" - --ploidy "${options_type.section_population_model_type.ploidy}" - ${options_type.section_population_model_type.pooled} - #end if - - ##reference allele - #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele": - --use-reference-allele - ${options_type.use_reference_allele_type.diploid_reference} - --reference-quality "${options_type.use_reference_allele_type.reference_quality_mq},${options_type.use_reference_allele_type.reference_quality_bq}" - #end if - - ##allele scope - #if str( $options_type.section_allele_scope_type.section_allele_scope_type_selector ) == "set": - ${options_type.section_allele_scope_type.no_snps} - ${options_type.section_allele_scope_type.no_indels} - ${options_type.section_allele_scope_type.no_mnps} - ${options_type.section_allele_scope_type.no_complex} - --use-best-n-alleles "${options_type.section_allele_scope_type.use_best_n_alleles}" - #if $options_type.section_allele_scope_type.max_complex_gap: - --max-complex-gap "${options_type.section_allele_scope_type.max_complex_gap}" - #end if - #end if - - ##indel realignment - ${options_type.left_align_indels} - - ##input filters - #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set": - ${options_type.section_input_filters_type.use_duplicate_reads} - #if str( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters": - --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}" - --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}" - --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}" - #else: - --no-filters - #end if - --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}" - #if $options_type.section_input_filters_type.read_mismatch_limit: - --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}" - #end if - --read-max-mismatch-fraction "${options_type.section_input_filters_type.read_max_mismatch_fraction}" - #if $options_type.section_input_filters_type.read_snp_limit: - --read-snp-limit "${options_type.section_input_filters_type.read_snp_limit}" - #end if - #if $options_type.section_input_filters_type.read_indel_limit: - --read-indel-limit "${options_type.section_input_filters_type.read_indel_limit}" - #end if - --indel-exclusion-window "${options_type.section_input_filters_type.indel_exclusion_window}" - --min-alternate-fraction "${options_type.section_input_filters_type.min_alternate_fraction}" - --min-alternate-count "${options_type.section_input_filters_type.min_alternate_count}" - --min-alternate-qsum "${options_type.section_input_filters_type.min_alternate_qsum}" - --min-alternate-total "${options_type.section_input_filters_type.min_alternate_total}" - --min-coverage "${options_type.section_input_filters_type.min_coverage}" - #end if - - ##bayesian priors - #if str( $options_type.section_bayesian_priors_type.section_bayesian_priors_type_selector ) == "set": - ${options_type.section_bayesian_priors_type.no_ewens_priors} - ${options_type.section_bayesian_priors_type.no_population_priors} - ${options_type.section_bayesian_priors_type.hwe_priors} - #end if - - ##observation prior expectations - #if str( $options_type.section_observation_prior_expectations_type.section_observation_prior_expectations_type_selector ) == "set": - ${options_type.section_observation_prior_expectations_type.binomial_obs_priors} - ${options_type.section_observation_prior_expectations_type.allele_balance_priors} - #end if - - ##algorithmic features - #if str( $options_type.section_algorithmic_features_type.section_algorithmic_features_type_selector ) == "set": - --site-selection-max-iterations "${options_type.section_algorithmic_features_type.site_selection_max_iterations}" - --genotyping-max-iterations "${options_type.section_algorithmic_features_type.genotyping_max_iterations}" - --genotyping-max-banddepth "${options_type.section_algorithmic_features_type.genotyping_max_banddepth}" - --posterior-integration-limits "${options_type.section_algorithmic_features_type.posterior_integration_limits_n},${options_type.section_algorithmic_features_type.posterior_integration_limits_m}" - ${options_type.section_algorithmic_features_type.no_permute} - ${options_type.section_algorithmic_features_type.exclude_unobserved_genotypes} - #if $options_type.section_algorithmic_features_type.genotype_variant_threshold: - --genotype-variant-threshold "${options_type.section_algorithmic_features_type.genotype_variant_threshold}" - #end if - ${options_type.section_algorithmic_features_type.use_mapping_quality} - --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}" - ${options_type.section_algorithmic_features_type.no_marginals} - #end if - - #end if - </command> - <inputs> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="cached"> - <repeat name="input_bams" title="Sample BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> - </param> - </repeat> - <param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="sam_fa_indexes"> -  - </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - </when> - <when value="history"> - <repeat name="input_bams" title="Sample BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> - </repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> - </when> - </conditional> - - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Basic or Advanced options"> - <option value="basic" selected="True">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic"> -  - </when> - <when value="advanced"> - -  - <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" /> - <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" /> - - -  - <conditional name="target_limit_type"> - <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"> - <option value="do_not_limit" selected="True">Do not limit</option> - <option value="limit_by_target_file">Limit by target file</option> - <option value="limit_by_region">Limit to region</option> - </param> - <when value="do_not_limit"> -  - </when> - <when value="limit_by_target_file"> - <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." /> - </when> - <when value="limit_by_region"> - <param name="region_chromosome" type="text" label="Region Chromosome" value="" /> - <param name="region_start" type="integer" label="Region Start" value="" /> - <param name="region_end" type="integer" label="Region End" value="" /> - </when> - </conditional> - <param name="input_sample_file" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" /> - <param name="input_populations_file" type="data" format="txt" label="Populations File" optional="True" /> - <param name="input_cnv_map_bed" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" /> - <conditional name="input_variant_type"> - <param name="input_variant_type_selector" type="select" label="Provide variants file"> - <option value="do_not_provide" selected="True">Do not provide</option> - <option value="provide_vcf">Provide VCF file</option> - </param> - <when value="do_not_provide"> -  - </when> - <when value="provide_vcf"> - <param name="input_variant_vcf" type="data" format="vcf" label="Use variants reported in VCF file as input to the algorithm" /> - <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> - </when> - </conditional> - - -  - <conditional name="section_reporting_type"> - <param name="section_reporting_type_selector" type="select" label="Set Reporting options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="pvar" type="float" label="Report sites if the probability that there is a polymorphism at the site is greater" value="0.0001" /> - <param name="show_reference_repeats" type="boolean" truevalue="--show-reference-repeats" falsevalue="" checked="False" label="Calculate and show information about reference repeats" /> - </when> - </conditional> - - -  - <conditional name="section_population_model_type"> - <param name="section_population_model_type_selector" type="select" label="Set population model options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="theta" type="float" label="expected mutation rate or pairwise nucleotide diversity among the population" value="0.001" help="This serves as the single parameter to the Ewens Sampling Formula prior model"/> - <param name="ploidy" type="integer" label="default ploidy for the analysis" value="2" /> - <param name="pooled" type="boolean" truevalue="--pooled" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing" help="When using this flag, set --ploidy to the number of alleles in each sample." /> - </when> - </conditional> - -  - <conditional name="use_reference_allele_type"> - <param name="use_reference_allele_type_selector" type="select" label="Include the reference allele in the analysis"> - <option value="do_not_include_reference_allele" selected="True">Do not include</option> - <option value="include_reference_allele">Include</option> - </param> - <when value="do_not_include_reference_allele"> -  - </when> - <when value="include_reference_allele"> - <param name="diploid_reference" type="boolean" truevalue="--diploid-reference" falsevalue="" checked="False" label="Treat reference as diploid" /> - <param name="reference_quality_mq" type="integer" label="Assign mapping quality" value="100" /> - <param name="reference_quality_bq" type="integer" label="Assign base quality" value="60" /> - </when> - </conditional> - -  - <conditional name="section_allele_scope_type"> - <param name="section_allele_scope_type_selector" type="select" label="Set allele scope options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="no_snps" type="boolean" truevalue="--no-snps" falsevalue="" checked="False" label="Ignore SNP alleles" /> - <param name="no_indels" type="boolean" truevalue="--no-indels" falsevalue="" checked="False" label="Ignore insertion and deletion alleles" /> - <param name="no_mnps" type="boolean" truevalue="--no-mnps" falsevalue="" checked="False" label="Ignore multi-nuceotide polymorphisms, MNPs" /> - <param name="no_complex" type="boolean" truevalue="--no-complex" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)" /> - <param name="use_best_n_alleles" type="integer" label="Evaluate only the best N SNP alleles" value="0" min="0" help="Ranked by sum of supporting quality scores; Set to 0 to use all" /> - <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/> - </when> - </conditional> - -  - <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left-realign and merge gaps embedded in reads" /> - -  - <conditional name="section_input_filters_type"> - <param name="section_input_filters_type_selector" type="select" label="Set input filters options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" /> - <conditional name="no_filter_type"> - <param name="no_filter_type_selector" type="select" label="Apply filters"> - <option value="apply_filters" selected="True">Apply</option> - <option value="no_filters">Do not apply</option> - </param> - <when value="no_filters"> -  - </when> - <when value="apply_filters"> - <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="30" /> - <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" /> - <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" /> - <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" /> - </when> - </conditional> - <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is >=" value="10" /> - <param name="read_mismatch_limit" type="integer" label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold" value="" optional="True" /> - <param name="read_max_mismatch_fraction" type="float" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold" value="1.0" /> - <param name="read_snp_limit" type="integer" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold" value="" optional="True" /> - <param name="read_indel_limit" type="integer" label="Exclude reads with more than N separate gaps" value="" optional="True" /> - <param name="indel_exclusion_window" type="integer" label="Ignore portions of alignments this many bases from a putative insertion or deletion allele" value="0" /> - <param name="min_alternate_fraction" type="float" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" value="0" /> - <param name="min_alternate_count" type="integer" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" value="1" /> - <param name="min_alternate_qsum" type="integer" label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" value="0" /> - <param name="min_alternate_total" type="integer" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" value="1" /> - <param name="min_coverage" type="integer" label="Require at least this coverage to process a site" value="0" /> - </when> - </conditional> - - -  - <conditional name="section_bayesian_priors_type"> - <param name="section_bayesian_priors_type_selector" type="select" label="Set bayesian priors options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="no_ewens_priors" type="boolean" truevalue="--no-ewens-priors" falsevalue="" checked="False" label="Turns off the Ewens' Sampling Formula component of the priors" /> - <param name="no_population_priors" type="boolean" truevalue="--no-population-priors" falsevalue="" checked="False" label="No population priors" help="Equivalent to --pooled --no-ewens-priors" /> - <param name="hwe_priors" type="boolean" truevalue="--hwe-priors" falsevalue="" checked="False" label="Use the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" /> - </when> - </conditional> - -  - <conditional name="section_observation_prior_expectations_type"> - <param name="section_observation_prior_expectations_type_selector" type="select" label="Set observation prior expectations options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="binomial_obs_priors" type="boolean" truevalue="--binomial-obs-priors" falsevalue="" checked="False" label="Incorporate expectations about osbervations into the priors, Uses read placement probability, strand balance probability, and read position (5'-3') probability" /> - <param name="allele_balance_priors" type="boolean" truevalue="--allele-balance-priors" falsevalue="" checked="False" label="Use aggregate probability of observation balance between alleles as a component of the priors. Best for observations with minimal inherent reference bias" /> - </when> - </conditional> - - -  - <conditional name="section_algorithmic_features_type"> - <param name="section_algorithmic_features_type_selector" type="select" label="Set algorithmic features options"> - <option value="do_not_set" selected="True">Do not set</option> - <option value="set">Set</option> - </param> - <when value="do_not_set"> -  - </when> - <when value="set"> - <param name="site_selection_max_iterations" type="integer" label="Uses hill-climbing algorithm to search posterior space for N iterations to determine if the site should be evaluated." value="5" help="Set to 0 to prevent use of this algorithm for site selection, and to a low integer for improvide site selection at a slight performance penalty" /> - <param name="genotyping_max_iterations" type="integer" label="Iterate no more than N times during genotyping step" value="25" /> - <param name="genotyping_max_banddepth" type="integer" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" value="6" /> - <param name="posterior_integration_limits_n" type="integer" label="Posteriror integration limit N" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="1" /> - <param name="posterior_integration_limits_m" type="integer" label="Posteriror integration limit M" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="3" /> - <param name="no_permute" type="boolean" truevalue="--no-permute" falsevalue="" checked="False" label="Do not scale prior probability of genotype combination given allele frequency by the number of permutations of included genotypes" /> - <param name="exclude_unobserved_genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" /> - <param name="genotype_variant_threshold" type="integer" label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample" value="" optional="True" /> - <param name="use_mapping_quality" type="boolean" truevalue="--use-mapping-quality" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods" /> - <param name="read_dependence_factor" type="float" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" value="0.9" /> - <param name="no_marginals" type="boolean" truevalue="--no-marginals" falsevalue="" checked="False" label="Do not calculate the marginal probability of genotypes. Saves time and improves scaling performance in large populations" /> - </when> - </conditional> - - - </when> - </conditional> - - </inputs> - <outputs> - <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> - <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> - <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter> - </data> - <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)"> - <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter> - </data> - </outputs> - <tests> - <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="phiX.fasta"/> - <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/> - <param name="options_type_selector" value="basic"/> - <output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> -  - </test> - </tests> - <help> -**What it does** - -This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file. - -FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners. - -In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. - -Go `here <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_ for details on FreeBayes. - ------- - -**Inputs** - -FreeBayes accepts an input aligned BAM file. - - -**Outputs** - -The output is in the VCF format. - -------- - -**Settings**:: - - input and output: - - -b --bam FILE Add FILE to the set of BAM files to be analyzed. - -c --stdin Read BAM input on stdin. - -v --vcf FILE Output VCF-format results to FILE. - -f --fasta-reference FILE - Use FILE as the reference sequence for analysis. - An index file (FILE.fai) will be created if none exists. - If neither --targets nor --region are specified, FreeBayes - will analyze every position in this reference. - -t --targets FILE - Limit analysis to targets listed in the BED-format FILE. - -r --region <chrom>:<start_position>..<end_position> - Limit analysis to the specified region, 0-base coordinates, - end_position not included (same as BED format). - -s --samples FILE - Limit analysis to samples listed (one per line) in the FILE. - By default FreeBayes will analyze all samples in its input - BAM files. - --populations FILE - Each line of FILE should list a sample and a population which - it is part of. The population-based bayesian inference model - will then be partitioned on the basis of the populations. - -A --cnv-map FILE - Read a copy number map from the BED file FILE, which has - the format: - reference sequence, start, end, sample name, copy number - ... for each region in each sample which does not have the - default copy number as set by --ploidy. - -L --trace FILE Output an algorithmic trace to FILE. - --failed-alleles FILE - Write a BED file of the analyzed positions which do not - pass --pvar to FILE. - -@ --variant-input VCF - Use variants reported in VCF file as input to the algorithm. - A report will be generated for every record in the VCF file. - -l --only-use-input-alleles - Only provide variant calls and genotype likelihoods for sites - and alleles which are provided in the VCF input, and provide - output in the VCF for all input alleles, not just those which - have support in the data. - - reporting: - - -P --pvar N Report sites if the probability that there is a polymorphism - at the site is greater than N. default: 0.0001 - -_ --show-reference-repeats - Calculate and show information about reference repeats in - the VCF output. - - population model: - - -T --theta N The expected mutation rate or pairwise nucleotide diversity - among the population under analysis. This serves as the - single parameter to the Ewens Sampling Formula prior model - default: 0.001 - -p --ploidy N Sets the default ploidy for the analysis to N. default: 2 - -J --pooled Assume that samples result from pooled sequencing. - When using this flag, set --ploidy to the number of - alleles in each sample. - - reference allele: - - -Z --use-reference-allele - This flag includes the reference allele in the analysis as - if it is another sample from the same population. - -H --diploid-reference - If using the reference sequence as a sample (-Z), - treat it as diploid. default: false (reference is haploid) - --reference-quality MQ,BQ - Assign mapping quality of MQ to the reference allele at each - site and base quality of BQ. default: 100,60 - - allele scope: - - -I --no-snps Ignore SNP alleles. - -i --no-indels Ignore insertion and deletion alleles. - -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs. - -u --no-complex Ignore complex events (composites of other classes). - -n --use-best-n-alleles N - Evaluate only the best N SNP alleles, ranked by sum of - supporting quality scores. (Set to 0 to use all; default: all) - -E --max-complex-gap N - Allow complex alleles with contiguous embedded matches of up - to this length. - - indel realignment: - - -O --left-align-indels - Left-realign and merge gaps embedded in reads. default: false - - input filters: - - -4 --use-duplicate-reads - Include duplicate-marked alignments in the analysis. - default: exclude duplicates - -m --min-mapping-quality Q - Exclude alignments from analysis if they have a mapping - quality less than Q. default: 30 - -q --min-base-quality Q - Exclude alleles from analysis if their supporting base - quality is less than Q. default: 20 - -R --min-supporting-quality MQ,BQ - In order to consider an alternate allele, at least one supporting - alignment must have mapping quality MQ, and one supporting - allele must have base quality BQ. default: 0,0, unset - -Q --mismatch-base-quality-threshold Q - Count mismatches toward --read-mismatch-limit if the base - quality of the mismatch is >= Q. default: 10 - -U --read-mismatch-limit N - Exclude reads with more than N mismatches where each mismatch - has base quality >= mismatch-base-quality-threshold. - default: ~unbounded - -z --read-max-mismatch-fraction N - Exclude reads with more than N [0,1] fraction of mismatches where - each mismatch has base quality >= mismatch-base-quality-threshold - default: 1.0 - -$ --read-snp-limit N - Exclude reads with more than N base mismatches, ignoring gaps - with quality >= mismatch-base-quality-threshold. - default: ~unbounded - -e --read-indel-limit N - Exclude reads with more than N separate gaps. - default: ~unbounded - -0 --no-filters Do not use any input base and mapping quality filters - Equivalent to -m 0 -q 0 -R 0 -S 0 - -x --indel-exclusion-window - Ignore portions of alignments this many bases from a - putative insertion or deletion allele. default: 0 - -F --min-alternate-fraction N - Require at least this fraction of observations supporting - an alternate allele within a single individual in the - in order to evaluate the position. default: 0.0 - -C --min-alternate-count N - Require at least this count of observations supporting - an alternate allele within a single individual in order - to evaluate the position. default: 1 - -3 --min-alternate-qsum N - Require at least this sum of quality of observations supporting - an alternate allele within a single individual in order - to evaluate the position. default: 0 - -G --min-alternate-total N - Require at least this count of observations supporting - an alternate allele within the total population in order - to use the allele in analysis. default: 1 - -! --min-coverage N - Require at least this coverage to process a site. default: 0 - - bayesian priors: - - -Y --no-ewens-priors - Turns off the Ewens' Sampling Formula component of the priors. - -k --no-population-priors - Equivalent to --pooled --no-ewens-priors - -w --hwe-priors Use the probability of the combination arising under HWE given - the allele frequency as estimated by observation frequency. - - observation prior expectations: - - -V --binomial-obs-priors - Incorporate expectations about osbervations into the priors, - Uses read placement probability, strand balance probability, - and read position (5'-3') probability. - -a --allele-balance-priors - Use aggregate probability of observation balance between alleles - as a component of the priors. Best for observations with minimal - inherent reference bias. - - algorithmic features: - - -M --site-selection-max-iterations N - Uses hill-climbing algorithm to search posterior space for N - iterations to determine if the site should be evaluated. Set to 0 - to prevent use of this algorithm for site selection, and - to a low integer for improvide site selection at a slight - performance penalty. default: 5. - -B --genotyping-max-iterations N - Iterate no more than N times during genotyping step. default: 25. - --genotyping-max-banddepth N - Integrate no deeper than the Nth best genotype by likelihood when - genotyping. default: 6. - -W --posterior-integration-limits N,M - Integrate all genotype combinations in our posterior space - which include no more than N samples with their Mth best - data likelihood. default: 1,3. - -K --no-permute - Do not scale prior probability of genotype combination given allele - frequency by the number of permutations of included genotypes. - -N --exclude-unobserved-genotypes - Skip sample genotypings for which the sample has no supporting reads. - -S --genotype-variant-threshold N - Limit posterior integration to samples where the second-best - genotype likelihood is no more than log(N) from the highest - genotype likelihood for the sample. default: ~unbounded - -j --use-mapping-quality - Use mapping quality of alleles when calculating data likelihoods. - -D --read-dependence-factor N - Incorporate non-independence of reads by scaling successive - observations by this factor during data likelihood - calculations. default: 0.9 - -= --no-marginals - Do not calculate the marginal probability of genotypes. Saves - time and improves scaling performance in large populations. - - ------- - -**Citation** - -For the underlying tool, please cite `FreeBayes <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_. - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix duplicate inclusion of tipsy library in base panels.
by Bitbucket 10 Jul '12

10 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d07c00d96b60/ changeset: d07c00d96b60 user: jgoecks date: 2012-07-10 18:44:35 summary: Fix duplicate inclusion of tipsy library in base panels. affected #: 2 files diff -r 7dcea1c1c833dac37844430180db6705d4846aa3 -r d07c00d96b60746a1e83713530a9070bf818e16c templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -5,7 +5,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.tipsy" )} </%def> ## Masthead diff -r 7dcea1c1c833dac37844430180db6705d4846aa3 -r d07c00d96b60746a1e83713530a9070bf818e16c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -5,7 +5,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.tipsy" )} </%def> ## Masthead Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes for installing tool shed repositories that include proprietary datatypes.
by Bitbucket 10 Jul '12

10 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7dcea1c1c833/ changeset: 7dcea1c1c833 user: greg date: 2012-07-10 17:38:32 summary: Fixes for installing tool shed repositories that include proprietary datatypes. affected #: 6 files diff -r 761a17ad3aad454283abca2bf33866ad954a2d97 -r 7dcea1c1c833dac37844430180db6705d4846aa3 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -190,9 +190,11 @@ except: pass if 'datatypes' in metadata_dict: - update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ) + tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES + if not tool_shed_repository.includes_datatypes: + tool_shed_repository.includes_datatypes = True + self.app.sa_session.add( tool_shed_repository ) + self.app.sa_session.flush() work_dir = make_tmp_directory() datatypes_config = get_config_from_repository( self.app, 'datatypes_conf.xml', diff -r 761a17ad3aad454283abca2bf33866ad954a2d97 -r 7dcea1c1c833dac37844430180db6705d4846aa3 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -309,6 +309,15 @@ for filename in sample_files: if filename not in sample_files_copied: copy_sample_file( app, filename, dest_path=dest_path ) +def create_repo_info_dict( repository, owner, repository_clone_url, changeset_revision, ctx_rev, metadata ): + repo_info_dict = {} + repo_info_dict[ repository.name ] = ( repository.description, + repository_clone_url, + changeset_revision, + ctx_rev, + owner, + metadata.get( 'tool_dependencies', None ) ) + return repo_info_dict def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): return dict( tool_shed=tool_shed, repository_name=name, diff -r 761a17ad3aad454283abca2bf33866ad954a2d97 -r 7dcea1c1c833dac37844430180db6705d4846aa3 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1,7 +1,7 @@ """ Contains functionality needed in every web interface """ -import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess +import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess, operator from datetime import date, datetime, timedelta from time import strftime from galaxy import config, tools, web, util @@ -177,6 +177,14 @@ def not_implemented( self, trans, **kwd ): raise HTTPNotImplemented() +class Datatype( object ): + """Used for storing in-memory list of datatypes currently in the datatypes registry.""" + def __init__( self, extension, dtype, type_extension, mimetype, display_in_upload ): + self.extension = extension + self.dtype = dtype + self.type_extension = type_extension + self.mimetype = mimetype + self.display_in_upload = display_in_upload # # -- Mixins for working with Galaxy objects. -- # @@ -2722,3 +2730,18 @@ return trans.environ[ 'webapp' ] # The default is galaxy. return 'galaxy' +def sort_by_attr( seq, attr ): + """ + Sort the sequence of objects by object's attribute + Arguments: + seq - the list or any sequence (including immutable one) of objects to sort. + attr - the name of attribute to sort by + """ + # Use the "Schwartzian transform" + # Create the auxiliary list of tuples where every i-th tuple has form + # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not + # only to provide stable sorting, but mainly to eliminate comparison of objects + # (which can be expensive or prohibited) in case of equal attribute values. + intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) + intermed.sort() + return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) diff -r 761a17ad3aad454283abca2bf33866ad954a2d97 -r 7dcea1c1c833dac37844430180db6705d4846aa3 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -605,7 +605,8 @@ tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] else: tool_section = None - for tool_shed_repository, repo_info_dict in zip( tool_shed_repositories, repo_info_dicts ): + for tup in zip( tool_shed_repositories, repo_info_dicts ): + tool_shed_repository, repo_info_dict = tup # Clone each repository to the configured location. update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] @@ -670,37 +671,6 @@ shutil.rmtree( work_dir ) except: pass - if 'datatypes' in metadata: - update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ) - work_dir = make_tmp_directory() - datatypes_config = get_config_from_repository( trans.app, - 'datatypes_conf.xml', - tool_shed_repository, - tool_shed_repository.installed_changeset_revision, - work_dir ) - # Load proprietary data types required by tools. - converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, relative_install_dir, override=False ) - if converter_path or display_path: - # Create a dictionary of tool shed repository related information. - repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, - name=tool_shed_repository.name, - owner=tool_shed_repository.owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) - if converter_path: - # Load proprietary datatype converters - trans.app.datatypes_registry.load_datatype_converters( trans.app.toolbox, installed_repository_dict=repository_dict ) - if display_path: - # Load proprietary datatype display applications - trans.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) - try: - shutil.rmtree( work_dir ) - except: - pass update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -749,9 +719,11 @@ except: pass if 'datatypes' in metadata_dict: - update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ) + tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES + if not tool_shed_repository.includes_datatypes: + tool_shed_repository.includes_datatypes = True + trans.sa_session.add( tool_shed_repository ) + trans.sa_session.flush() work_dir = make_tmp_directory() datatypes_config = get_config_from_repository( trans.app, 'datatypes_conf.xml', @@ -1255,13 +1227,12 @@ repo_info_dict = kwd.get( 'repo_info_dict', None ) if not repo_info_dict: # This should only happen if the tool_shed_repository does not include any valid tools. - repo_info_dict = {} - repo_info_dict[ tool_shed_repository.name ] = ( tool_shed_repository.description, - repository_clone_url, - tool_shed_repository.installed_changeset_revision, - ctx_rev, - tool_shed_repository.owner, - metadata.get( 'tool_dependencies', None ) ) + repo_info_dict = create_repo_info_dict( tool_shed_repository, + tool_shed_repository.owner, + repository_clone_url, + tool_shed_repository.installed_changeset_revision, + ctx_rev, + metadata ) new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, install_tool_dependencies=install_tool_dependencies, @@ -1291,7 +1262,8 @@ if ids is not None and status_list is not None: ids = util.listify( ids ) status_list = util.listify( status_list ) - for id, status in zip( ids, status_list ): + for tup in zip( ids, status_list ): + id, status = tup repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) if repository.status != status: rval.append( dict( id=id, @@ -1335,13 +1307,12 @@ tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) ctx_rev = get_ctx_rev( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision ) repository_clone_url = generate_clone_url( trans, repository ) - repo_info_dict = {} - repo_info_dict[ repository.name ] = ( repository.description, - repository_clone_url, - repository.installed_changeset_revision, - ctx_rev, - repository.owner, - metadata.get( 'tool_dependencies', None ) ) + repo_info_dict = create_repo_info_dict( repository, + repository.owner, + repository_clone_url, + repository.installed_changeset_revision, + ctx_rev, + metadata ) # Get the location in the tool panel in which the tool was originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -1419,7 +1390,8 @@ if ids is not None and status_list is not None: ids = util.listify( ids ) status_list = util.listify( status_list ) - for id, status in zip( ids, status_list ): + for tup in zip( ids, status_list ): + id, status = tup tool_dependency = trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) if tool_dependency.status != status: rval.append( dict( id=id, diff -r 761a17ad3aad454283abca2bf33866ad954a2d97 -r 7dcea1c1c833dac37844430180db6705d4846aa3 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,7 +9,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, make_tmp_directory, NOT_TOOL_CONFIGS +from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, make_tmp_directory, NOT_TOOL_CONFIGS from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path from galaxy.tool_shed.encoding_util import * from common import * @@ -931,29 +931,6 @@ trans.sa_session.flush() download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str ) return trans.response.send_redirect( download_url ) - def __encode_repo_info_dict( self, trans, repository_metadata_ids ): - repo_info_dict = {} - includes_tools = False - includes_tool_dependencies = False - for repository_metadata_id in util.listify( repository_metadata_ids ): - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - if not includes_tools and 'tools' in repository_metadata.metadata: - includes_tools = True - if not includes_tool_dependencies and 'tool_dependencies' in repository_metadata.metadata: - includes_tool_dependencies = True - repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) - # Get the changelog rev for this changeset_revision. - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( repo, changeset_revision ) - repository_id = trans.security.encode_id( repository.id ) - repository_clone_url = generate_clone_url( trans, repository_id ) - if includes_tool_dependencies: - repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) ) - else: - repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) ) - return tool_shed_encode( repo_info_dict ), includes_tools, includes_tool_dependencies @web.expose def find_tools( self, trans, **kwd ): params = util.Params( kwd ) @@ -1156,7 +1133,8 @@ includes_tools = False includes_tool_dependencies = False repo_info_dicts = [] - for repository_id, changeset_revision in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): + for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): + repository_id, changeset_revision = tup repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1168,15 +1146,8 @@ repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = {} - repo_info_dict[ repository.name ] = ( repository.description, - repository_clone_url, - changeset_revision, - str( ctx.rev() ), - repository.user.username, - metadata.get( 'tool_dependencies', None ) ) - encoded_repo_info_dict = tool_shed_encode( repo_info_dict ) - repo_info_dicts.append( encoded_repo_info_dict ) + repo_info_dict = create_repo_info_dict( repository, repository.user.username, repository_clone_url, changeset_revision, str( ctx.rev() ), metadata ) + repo_info_dicts.append( tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) @web.expose def get_readme( self, trans, **kwd ): diff -r 761a17ad3aad454283abca2bf33866ad954a2d97 -r 7dcea1c1c833dac37844430180db6705d4846aa3 templates/admin/view_datatypes_registry.mako --- a/templates/admin/view_datatypes_registry.mako +++ b/templates/admin/view_datatypes_registry.mako @@ -5,8 +5,24 @@ ${render_msg( message, status )} %endif +<% + import galaxy.util + from galaxy.web.base.controller import sort_by_attr, Datatype + ctr = 0 + datatypes = [] + for elem in trans.app.datatypes_registry.datatype_elems: + # Build a list of objects that can be sorted. + extension = elem.get( 'extension', None ) + dtype = elem.get( 'type', None ) + type_extension = elem.get( 'type_extension', None ) + mimetype = elem.get( 'mimetype', None ) + display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) + datatypes.append( Datatype( extension, dtype, type_extension, mimetype, display_in_upload ) ) + sorted_datatypes = sort_by_attr( datatypes, 'extension' ) +%> + <div class="toolForm"> - <div class="toolFormTitle">Current datatypes registry contains ${len( trans.app.datatypes_registry.datatype_elems )} datatypes</div> + <div class="toolFormTitle">Current datatypes registry contains ${len( sorted_datatypes )} datatypes</div><div class="toolFormBody"><table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr> @@ -14,33 +30,23 @@ <th>Type</th><th>Mimetype</th><th>Display in upload</th> - <th>Datatype class</th></tr> - <% ctr = 0 %> - %for elem in trans.app.datatypes_registry.datatype_elems: - <% - import galaxy.util - extension = elem.get( 'extension', None ) - dtype = elem.get( 'type', None ) - type_extension = elem.get( 'type_extension', None ) - mimetype = elem.get( 'mimetype', None ) - display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) - %> + %for datatype in sorted_datatypes: %if ctr % 2 == 1: <tr class="odd_row"> %else: <tr class="tr"> %endif - <td>${extension}</td> - <td>${dtype}</td> + <td>${datatype.extension}</td> + <td>${datatype.dtype}</td><td> - %if mimetype: - ${mimetype} + %if datatype.mimetype: + ${datatype.mimetype} %endif </td><td> - %if display_in_upload: - ${display_in_upload} + %if datatype.display_in_upload: + ${datatype.display_in_upload} %endif </td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits July 2012