- galaxy-dev - lists.galaxyproject.org

galaxy server configuration questions
by Assaf Gordon 27 Jun '09

27 Jun '09

Hello, I have two small questions regarding galaxy server configuration: 1. The Galaxy Cookie. Sometimes I see a fixed 'galaxysession' cookie, and other times I see a cookie with the name set in 'universe_wsgi.ini' as the "session_key". I'm not sure when is each one used. What I'd like to do is run two galaxy servers on the server - I don't want to cookies to interfere with one another. (could it have something with using or not using external authentication?) 2. setting path of Galaxy's file: There's the big 'database' directory. Inside it, there are: files, import, pbs, job_working_directory, beaker_sessions, tmp, compiled_templates. Some of those are changeable from the universe_wsgi.ini, (e.g. files, tmp, beaker_sessions) but others are not ( job_working_directory, compiled_templates). Is there a way to change those path ? I'd like to have the galaxy source code in a completely read-only location, and all of the runtime files in "/var/galaxy". However, one the 'galaxy' base directory is read only, I get several 'permission denied' exceptions when I try to use the galaxy server. Thanks, Gordon.

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[hg] galaxy 2459: New packed scripts
by Nate Coraor 26 Jun '09

26 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b26e2ef8726c changeset: 2459:b26e2ef8726c user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jun 26 09:22:31 2009 -0400 description: New packed scripts 5 file(s) affected in this change: static/scripts/packed/galaxy.panels.js static/scripts/packed/jquery.event.drag.js static/scripts/packed/jquery.event.drop.js static/scripts/packed/jquery.js static/scripts/packed/trackster.js diffs (63 lines): diff -r 842af32c4e73 -r b26e2ef8726c static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Thu Jun 25 15:34:05 2009 -0400 +++ b/static/scripts/packed/galaxy.panels.js Fri Jun 26 09:22:31 2009 -0400 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragend ",function(i){$("#DD-helper").hide()}).bind("drag",function(i){x=i.offsetX;x=Math.min(400,Math.max(100,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(i){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false} ;var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide()})}function show_modal(f,c,e,d){$(".dialog-box").find(".title").html(f);var a=$(".dialog-box").find(".buttons").html("");if(e){$.each(e,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").f ind(".extra_buttons").html("");if(d){$.each(d,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}$(function(){$("span.tab").each(function(){var a=$(this).children("div.submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file +function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragend ",function(i){$("#DD-helper").hide()}).bind("drag",function(i){x=i.offsetX;x=Math.min(400,Math.max(100,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(i){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false} ;var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(f,c,e,d){if(f){$(".dialog-box").find(".title").html(f);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dia log-box").find(".buttons").html("");if(e){$.each(e,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"))}$(function(){$("span.tab").each(function(){var a=$(t his).children("div.submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file diff -r 842af32c4e73 -r b26e2ef8726c static/scripts/packed/jquery.event.drag.js --- a/static/scripts/packed/jquery.event.drag.js Thu Jun 25 15:34:05 2009 -0400 +++ b/static/scripts/packed/jquery.event.drag.js Fri Jun 26 09:22:31 2009 -0400 @@ -1,1 +1,5 @@ -(function(h){h.fn.drag=function(k,j,i){if(j){this.bind("dragstart",k)}if(i){this.bind("dragend",i)}return !k?this.trigger("drag"):this.bind("drag",j?j:k)};var d=h.event,b=d.special,f=b.drag={not:":input",distance:0,which:1,setup:function(i){i=h.extend({distance:f.distance,which:f.which,not:f.not},i||{});i.distance=g(i.distance);d.add(this,"mousedown",e,i)},teardown:function(){d.remove(this,"mousedown",e);if(this===f.dragging){f.dragging=f.proxy=null}c(this,true)}};function e(k){var j=this,i,l=k.data||{};if(l.elem){j=k.dragTarget=l.elem;k.dragProxy=f.proxy||j;k.cursorOffsetX=l.pageX-l.left;k.cursorOffsetY=l.pageY-l.top;k.offsetX=k.pageX-k.cursorOffsetX;k.offsetY=k.pageY-k.cursorOffsetY}else{if(f.dragging||(l.which>0&&k.which!=l.which)||h(k.target).is(l.not)){return}}switch(k.type){case"mousedown":h.extend(l,h(j).offset(),{elem:j,target:k.target,pageX:k.pageX,pageY:k.pageY});d.add(document,"mousemove mouseup",e,l);c(j,false);return false;case !f.dragging&&"mousemove":if(g(k.pa geX-l.pageX)+g(k.pageY-l.pageY)<l.distance){break}k.target=l.target;i=a(k,"dragstart",j);if(i!==false){f.dragging=j;f.proxy=k.dragProxy=h(i||j)[0]}case"mousemove":if(f.dragging){i=a(k,"drag",j);if(b.drop){b.drop.allowed=(i!==false);b.drop.handler(k)}if(i!==false){break}k.type="mouseup"}case"mouseup":d.remove(document,"mousemove mouseup",e);if(f.dragging){if(b.drop){b.drop.handler(k)}a(k,"dragend",j)}else{a(k,"dragclickonly",j)}c(j,true);f.dragging=f.proxy=l.elem=null;break}}function a(l,j,k){l.type=j;var i=d.handle.call(k,l);return i===false?false:i||l.result}function g(i){return Math.pow(i,2)}function c(j,i){if(!j){return}j.unselectable=i?"off":"on";j.onselectstart=function(){return i};if(document.selection&&document.selection.empty){document.selection.empty()}if(j.style){j.style.MozUserSelect=i?"":"none"}}})(jQuery); +/* +jquery.event.drag.js ~ v1.4 ~ Copyright (c) 2008, Three Dub Media (http://threedubmedia.com) +Liscensed under the MIT License ~ http://threedubmedia.googlecode.com/files/MIT-LICENSE.txt +*/ +(function(h){h.fn.drag=function(k,j,i){if(j){this.bind("dragstart",k)}if(i){this.bind("dragend",i)}return !k?this.trigger("drag"):this.bind("drag",j?j:k)};var d=h.event,b=d.special,f=b.drag={not:":input",distance:0,which:1,setup:function(i){i=h.extend({distance:f.distance,which:f.which,not:f.not},i||{});i.distance=g(i.distance);d.add(this,"mousedown",e,i)},teardown:function(){d.remove(this,"mousedown",e);if(this===f.dragging){f.dragging=f.proxy=null}c(this,true)}};function e(k){var j=this,i,l=k.data||{};if(l.elem){j=k.dragTarget=l.elem;k.dragProxy=f.proxy||j;k.cursorOffsetX=l.pageX-l.left;k.cursorOffsetY=l.pageY-l.top;k.offsetX=k.pageX-k.cursorOffsetX;k.offsetY=k.pageY-k.cursorOffsetY}else{if(f.dragging||(l.which>0&&k.which!=l.which)||h(k.target).is(l.not)){return}}switch(k.type){case"mousedown":h.extend(l,h(j).offset(),{elem:j,target:k.target,pageX:k.pageX,pageY:k.pageY});d.add(document,"mousemove mouseup",e,l);c(j,false);return false;case !f.dragging&&"mousemove":if(g(k.pa geX-l.pageX)+g(k.pageY-l.pageY)<l.distance){break}k.target=l.target;i=a(k,"dragstart",j);if(i!==false){f.dragging=j;f.proxy=k.dragProxy=h(i||j)[0]}case"mousemove":if(f.dragging){i=a(k,"drag",j);if(b.drop){b.drop.allowed=(i!==false);b.drop.handler(k)}if(i!==false){break}k.type="mouseup"}case"mouseup":d.remove(document,"mousemove mouseup",e);if(f.dragging){if(b.drop){b.drop.handler(k)}a(k,"dragend",j)}else{a(k,"dragclickonly",j)}c(j,true);f.dragging=f.proxy=l.elem=null;break}}function a(l,j,k){l.type=j;var i=d.handle.call(k,l);return i===false?false:i||l.result}function g(i){return Math.pow(i,2)}function c(j,i){if(!j){return}j.unselectable=i?"off":"on";j.onselectstart=function(){return i};if(document.selection&&document.selection.empty){document.selection.empty()}if(j.style){j.style.MozUserSelect=i?"":"none"}}})(jQuery); 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+/* jquery.event.drop.js * v1.2 +Copyright (c) 2008-2009, Three Dub Media (http://threedubmedia.com) +Liscensed under the MIT License (http://threedubmedia.googlecode.com/files/MIT-LICENSE.txt) +*/ +(function(f){f.fn.drop=function(i,h,g){if(h){this.bind("dropstart",i)}if(g){this.bind("dropend",g)}return !i?this.trigger("drop"):this.bind("drop",h?h:i)};f.dropManage=function(g){g=g||{};c.data=[];c.filter=g.filter||"*";c.delay=g.delay||c.delay;c.tolerance=g.tolerance||null;c.mode=g.mode||c.mode||"intersect";return c.$targets.filter(c.filter).each(function(){c.data[c.data.length]=c.locate(this)})};var d=f.event,b=d.special,c=b.drop={delay:100,mode:"intersect",$targets:f([]),data:[],setup:function(){c.$targets=c.$targets.add(this);c.data[c.data.length]=c.locate(this)},teardown:function(){var g=this;c.$targets=c.$targets.not(this);c.data=f.grep(c.data,function(h){return(h.elem!==g)})},handler:function(h){var g=null,i;h.dropTarget=c.dropping||undefined;if(c.data.length&&h.dragTarget){switch(h.type){case"drag":c.event=h;if(!c.timer){c.timer=setTimeout(e,20)}break;case"mouseup":c.timer=clearTimeout(c.timer);if(!c.dropping){break}if(c.allowed){i=a(h,"drop",c.dropping)}g=false;cas e c.dropping&&"dropstart":g=g===null&&c.allowed?true:false;case c.dropping&&"dropend":a(h,"dropend",c.dropping);c.dropping=null;if(i===false){h.dropTarget=undefined}if(!g){break}case c.allowed&&"dropstart":h.dropTarget=this;c.dropping=a(h,"dropstart",this)!==false?this:null;break}}},locate:function(k){var i=f(k),l=i.offset(),j=i.outerHeight(),g=i.outerWidth();return{elem:k,L:l.left,R:l.left+g,T:l.top,B:l.top+j,W:g,H:j}},contains:function(g,h){return((h[0]||h.L)>=g.L&&(h[0]||h.R)<=g.R&&(h[1]||h.T)>=g.T&&(h[1]||h.B)<=g.B)},modes:{intersect:function(h,g,i){return this.contains(i,[h.pageX,h.pageY])?i:this.modes.overlap.apply(this,arguments)},overlap:function(h,g,i){i.overlap=Math.max(0,Math.min(i.B,g.B)-Math.max(i.T,g.T))*Math.max(0,Math.min(i.R,g.R)-Math.max(i.L,g.L));if(i.overlap>((this.best||{}).overlap||0)){this.best=i}return null},fit:function(h,g,i){return this.contains(i,g)?i:null},middle:function(h,g,i){return this.contains(i,[g.L+g.W/2,g.T+g.H/2])?i:null}}};function a(k ,i,j){k.type=i;try{var g=d.handle.call(j,k)}catch(h){}return g===false?false:g||k.result}function e(){var h=0,g,j,k=[c.event.pageX,c.event.pageY],l=c.locate(c.event.dragProxy);c.tolerance=c.tolerance||c.modes[c.mode];do{if(g=c.data[h]){j=c.tolerance?c.tolerance.call(c,c.event,l,g):c.contains(g,k)?g:null}}while(++h<c.data.length&&!j);c.event.type=(j=j||c.best)?"dropstart":"dropend";if(c.event.type=="dropend"||j.elem!=c.dropping){c.handler.call(j?j.elem:c.dropping,c.event)}if(c.last&&k[0]==c.last.pageX&&k[1]==c.last.pageY){delete c.timer}else{c.timer=setTimeout(e,c.delay)}c.last=c.event;c.best=null}})(jQuery); 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l=false;m.beginPath();var t=k.values;for(var o=0;o<t.length-1;o++){var r=t[o][0]-s;var e=t[o][1];var p=t[o+1][0]-s;var c=t[o+1][1];if(isNaN(e)||isNaN(c)){l=false}else{r=r*j;p=p*j;e=h-e*(h);c=h-c*(h);if(l){m.lineTo(r,e,p,c)}else{m.moveTo(r,e,p,c);l=true}}}m.stroke();return b}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Ma th.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+a+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var itemHeight=13,itemPad=3,thinHeight=7,thinOffset=3;var 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View=function(b,c,a,d){this.chr=b;this.length=c;this.low=a;this.high=d};$.extend(View.prototype,{move:function(b,a){this.low=Math.max(0,Math.floor(b));this.high=Math.min(this.length,Math.ceil(a))},zoom_in:function(c){var a=(this.low+this.high)/2;var b=this.high-this.low;var d=b/c/2;this.low=Math.floor(a-d);this.high=Math.ceil(a+d);if(this.high-this.low<1){this.high=this.low+1}},zoom_out:function(c){var a=(this.low+this.high)/2;var b=this.high-this.low;var d=b*c/2;this.low=Math.floor(Math.max(0,a-d));this.high=Math.ceil(Math.min(this.length,a+d))},left:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.low-c<0){this.low=0;this.high=this.low+a}else{this.low-=c;this.high-=c}},right:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.high+c>this.length){this.high=this.length;this.low=this.high-a}else{this.low+=c;this.high+=c}}});var Track=function(b,a,c){this.name=b;this.view=a;this.parent_element=c;this.make_container()};$.ext 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ck.prototype,TiledTrack.prototype,{make_container:function(){Track.prototype.make_container.call(this);this.content_div.css("height",100)},draw_tile:function(n,q,g,j,h){var s=q*DENSITY*n,d=(q+1)*DENSITY*n,a=DENSITY*n;var k=this.cache.get(n,q);var b;if(k.state=="loading"){b=$("<div class='loading tile'></div>")}else{b=$("<canvas class='tile'></canvas>")}b.css({position:"absolute",top:0,left:(s-this.view.low)*j,width:Math.ceil(a*j),height:100});g.append(b);if(k.state=="loading"){l=false;return null}var f=b;f.get(0).width=f.width();f.get(0).height=f.height();var m=f.get(0).getContext("2d");var l=false;m.beginPath();var t=k.values;for(var o=0;o<t.length-1;o++){var r=t[o][0]-s;var e=t[o][1];var p=t[o+1][0]-s;var c=t[o+1][1];console.log(r,e,p,c);if(isNaN(e)||isNaN(c)){l=false}else{r=r*j;p=p*j;e=h-e*(h);c=h-c*(h);if(l){m.lineTo(r,e,p,c)}else{m.moveTo(r,e,p,c);l=true}}}m.stroke();return b}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.container_div.addClass("label-tr ack")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+a+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var itemHeight=13,itemPad=3,thinHeight=7,thinOffset=3;var FeatureTrack=function(c,b,d,a){Track.call(this,c,b,d);this.container_div.addClass("feature-track");this.dataset_id=a;this.cache=new DataCache("",this,b)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data_async:function(){var a=this;$.getJSON("data",{chr:this.view.chr,dataset_id:this.dataset_id},function(b){a.values=b;a.draw()})},draw_tile:function(x,y,h,m,l){var z=y*DENSITY*x,c=(y+1)*DENSITY*x,a=DENSITY*x;var q=this.view,s=q.high-q.low,u= this.content_div.width(),p=[],A=$("<div class='tile' style='position: relative;'></div>");var o=this.cache.get(x,y);if(o.state=="loading"){h.addClass("loading");return null}else{h.removeClass("loading")}var b=o.values;for(var k in b){var v=b[k];var f=v[1],e=v[2],t=v[5];var g=(f-z)*m;var n=(e-z)*m;var w=n-g;var j=g;var d=p.length;for(i in p){if(p[i]<j){d=i;break}}p[d]=Math.ceil(n);var r=$("<div class='feature'></div>").css({position:"absolute",left:g,top:(d*(itemHeight+itemPad)),height:itemHeight,width:Math.max(w,1)});A.append(r)}A.css({position:"absolute",top:0,left:(z-this.view.low)*m,width:Math.ceil(a*m),height:p.length*(itemHeight+itemPad)+itemPad});h.append(A);return A}});var TrackLayout=function(a){this.view=a;this.tracks=[]};$.extend(TrackLayout.prototype,{add:function(a){this.tracks.push(a)},redraw:function(){for(var a in this.tracks){this.tracks[a].draw()}$("#overview-box").css({left:(this.view.low/this.view.length)*$("#overview-viewport").width(),width:Math.max(1,(( this.view.high-this.view.low)/this.view.length)*$("#overview-viewport").width())}).show();$("#low").text(this.view.low);$("#high").text(this.view.high)}}); \ No newline at end of file

1 0

[hg] galaxy 2458: A tiny bug fix for Sort tool - the delimiter i...
by Nate Coraor 26 Jun '09

26 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/842af32c4e73 changeset: 2458:842af32c4e73 user: guru date: Thu Jun 25 15:34:05 2009 -0400 description: A tiny bug fix for Sort tool - the delimiter is now defaulted to tab. 2 file(s) affected in this change: tools/filters/sorter.py tools/filters/sorter.xml diffs (21 lines): diff -r 8dfe971fcc27 -r 842af32c4e73 tools/filters/sorter.py --- a/tools/filters/sorter.py Thu Jun 25 15:29:24 2009 -0400 +++ b/tools/filters/sorter.py Thu Jun 25 15:34:05 2009 -0400 @@ -103,7 +103,7 @@ # Launch sort. environ['LC_ALL'] = 'POSIX' - commandline = "sort -f"+style+"-k "+str(column)+" -o "+outputfile+" "+inputfile+order + commandline = "sort -f"+style+"-k "+str(column)+" -t $'\t' -o "+outputfile+" "+inputfile+order errorcode, stdout = commands.getstatusoutput(commandline) diff -r 8dfe971fcc27 -r 842af32c4e73 tools/filters/sorter.xml --- a/tools/filters/sorter.xml Thu Jun 25 15:29:24 2009 -0400 +++ b/tools/filters/sorter.xml Thu Jun 25 15:34:05 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="sort1" name="Sort"> +<tool id="sort1" name="Sort" version="1.0.1"> <description>data in ascending or descending order</description> <command interpreter="python">sorter.py -i $input -o $out_file1 -cols $column -order $order -style $style</command> <inputs>

1 0

[hg] galaxy 2457: Extract genomic DNA tool now uses only alignse...
by Nate Coraor 26 Jun '09

26 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8dfe971fcc27 changeset: 2457:8dfe971fcc27 user: guru date: Thu Jun 25 15:29:24 2009 -0400 description: Extract genomic DNA tool now uses only alignseq.loc to access sequence files. The twobit.loc file will henceforth be unnecessary, and all sequences from it should be moved to alignseq.loc. 1 file(s) affected in this change: tools/extract/extract_genomic_dna.py diffs (92 lines): diff -r d3abf05d9272 -r 8dfe971fcc27 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Fri Jun 19 11:21:13 2009 -0400 +++ b/tools/extract/extract_genomic_dna.py Thu Jun 25 15:29:24 2009 -0400 @@ -4,7 +4,7 @@ -1, --cols=N,N,N,N: Columns for start, end, strand in input file -d, --dbkey=N: Genome build of input file -o, --output_format=N: the data type of the output file - -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc and twobit.loc + -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc """ from galaxy import eggs import pkg_resources @@ -29,33 +29,20 @@ reversed_s.reverse() return "".join( reversed_s ) -def check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ): - nib_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR - nib_path = '' - for line in open( nib_file ): +def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ): + seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR + seq_path = '' + for line in open( seq_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: - nib_path = fields[2].strip() + seq_path = fields[2].strip() break - return nib_path + return seq_path -def check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ): - twobit_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR - twobit_path = '' - for line in open( twobit_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( "#" ): - fields = line.split( '\t' ) - if len( fields ) < 2: - continue - if fields[0] == dbkey: - twobit_path = fields[1].strip() - break - return twobit_path def __main__(): options, args = doc_optparse.parse( __doc__ ) @@ -72,9 +59,8 @@ strand = None nibs = {} twobits = {} - nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ) - twobit_path = check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ) - if not os.path.exists( nib_path ) and not os.path.exists( twobit_path ): + seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) + if not os.path.exists( seq_path ): # If this occurs, we need to fix the metadata validator. stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey ) @@ -116,11 +102,11 @@ strand = '+' sequence = '' - if nib_path and os.path.exists( "%s/%s.nib" % ( nib_path, chrom ) ): + if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ): if chrom in nibs: nib = nibs[chrom] else: - nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( nib_path, chrom ) ) ) + nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: sequence = nib.get( start, end-start ) except: @@ -131,11 +117,11 @@ first_invalid_line = i + 1 invalid_line = line continue - elif twobit_path and os.path.exists( twobit_path ): + elif seq_path and os.path.exists( seq_path ): if chrom in twobits: t = twobits[chrom] else: - twobits[chrom] = t = bx.seq.twobit.TwoBitFile( file( twobit_path ) ) + twobits[chrom] = t = bx.seq.twobit.TwoBitFile( file( seq_path ) ) try: sequence = t[chrom][start:end] except:

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OT: HTML output / Multiple Output files
by Assaf Gordon 26 Jun '09

26 Jun '09

Hello, I recently had to add a tool which generates a variable number of output files, and I used the HTML / output directory trick as (very concisely) explained here: http://g2.trac.bx.psu.edu/wiki/AddingToolsFAQ This is a very cool feature! It took some time to get right, so I'm attaching a complete working example for future reference (you can add it to the wiki, if you'd like). Using an <IFRAME> inside the output HTML, I can even show the multiple output files in the main HTML page, in a report-like way. Thanks, and keep up the good work. Gordon.

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TIP: Galaxy + MySql + SQLAlchemy
by Assaf Gordon 25 Jun '09

25 Jun '09

Hello, Here's a tip for connecting galaxy to mysql on localhost (if it didn't work for you out of the box): ## Get a clean copy of galaxy $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy ## Create dedicated MySQL database for galaxy, ## with user 'galaxy' and password '12345' $ mysql -u root -p password: mysql> create database galaxy ; mysql> use galaxy ; mysql> grant all on galaxy.* to 'galaxy'@'localhost' identified by '12345'; ## Setup Galaxy $ sh setup.sh ## Change universe_wsgi.ini, to use the new database database_connection = mysql://galaxy:12345@localhost/galaxy ## Run Galaxy $ sh run.sh ----------------- But here's the catch: On a standard debian system, mysql puts the unix socket file in /var/run/mysqld/mysqld.sock However, SqlAlchemy assumes the socket is in /tmp/mysql.sock. So when I run galaxy, I get the following exception: OperationalError: (OperationalError) (2002, "Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)") None None Two possible solutions for that: 1. Change the socket file in /etc/mysql/my.cnf (not recommended) or 2. Add the following incantation to the SQLAlchemy string in universe_wsgi.ini: database_connection = mysql://galaxy:12345@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock With this change, Galaxy runs fine with mysql on localhost. -Gordon.

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[hg] galaxy 2456: Fix for importing history items ( datasets ) t...
by Greg Von Kuster 20 Jun '09

20 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d3abf05d9272 changeset: 2456:d3abf05d9272 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jun 19 11:21:13 2009 -0400 description: Fix for importing history items ( datasets ) that include child datasets into a library. 1 file(s) affected in this change: lib/galaxy/model/__init__.py diffs (42 lines): diff -r 075c0fd5b1d5 -r d3abf05d9272 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Jun 18 12:10:36 2009 -0400 +++ b/lib/galaxy/model/__init__.py Fri Jun 19 11:21:13 2009 -0400 @@ -628,7 +628,7 @@ hda.set_peek() hda.flush() return hda - def to_library_dataset_dataset_association( self, target_folder, replace_dataset=None, parent_id=None ): + def to_library_dataset_dataset_association( self, target_folder, replace_dataset=None, parent_id=None, user=None ): if replace_dataset: # The replace_dataset param ( when not None ) refers to a LibraryDataset that is being replaced with a new version. library_dataset = replace_dataset @@ -637,6 +637,8 @@ # LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset. library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info ) library_dataset.flush() + if not user: + user = self.history.user ldda = LibraryDatasetDatasetAssociation( name=self.name, info=self.info, blurb=self.blurb, @@ -649,7 +651,7 @@ deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association=self, - user=self.history.user ) + user=user ) ldda.flush() # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset # Must set metadata after ldda flushed, as MetadataFiles require ldda.id @@ -660,7 +662,10 @@ library_dataset.library_dataset_dataset_association_id = ldda.id library_dataset.flush() for child in self.children: - child_copy = child.to_library_dataset_dataset_association( target_folder=target_folder, replace_dataset=replace_dataset, parent_id=ldda.id ) + child_copy = child.to_library_dataset_dataset_association( target_folder=target_folder, + replace_dataset=replace_dataset, + parent_id=ldda.id, + user=ldda.user ) if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs ldda.set_peek()

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[hg] galaxy 2455: Fix for detecting metadata column types in tab...
by Greg Von Kuster 19 Jun '09

19 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/075c0fd5b1d5 changeset: 2455:075c0fd5b1d5 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Jun 18 12:10:36 2009 -0400 description: Fix for detecting metadata column types in tabular files, the number of lines read for detecting column types will always be the max setting, with previously detected column types being overridden if appropriate ( e.g., int overridden with float ). This will only occur in files whose data varies between types within the same column. 1 file(s) affected in this change: lib/galaxy/datatypes/tabular.py diffs (14 lines): diff -r d83b9225b5dd -r 075c0fd5b1d5 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Tue Jun 16 13:54:33 2009 -0400 +++ b/lib/galaxy/datatypes/tabular.py Thu Jun 18 12:10:36 2009 -0400 @@ -121,8 +121,8 @@ #"column_types": ["int", "int", "str", "list"] first_line_column_types = column_types column_types = [ None for col in first_line_column_types ] - elif ( column_types and None not in column_types ) or i > num_check_lines: - #found and set all known columns, or we exceeded our max check lines + elif i > num_check_lines: + # We exceeded our max check lines break #we error on the larger number of columns

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[hg] galaxy 2454: Add the hostname of the Galaxy instance to err...
by Greg Von Kuster 19 Jun '09

19 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d83b9225b5dd changeset: 2454:d83b9225b5dd user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jun 16 13:54:33 2009 -0400 description: Add the hostname of the Galaxy instance to error reports. 2 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py lib/galaxy/web/framework/base.py diffs (54 lines): diff -r e899101e63d1 -r d83b9225b5dd lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Jun 16 09:55:15 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Jun 16 13:54:33 2009 -0400 @@ -16,7 +16,10 @@ GALAXY TOOL ERROR REPORT ------------------------ -This error report is in reference to output dataset ${dataset_id}. +This error report was sent from the Galaxy instance hosted on the server +"${remote_hostname}" +----------------------------------------------------------------------------- +This is in reference to output dataset ${dataset_id}. ----------------------------------------------------------------------------- The user '${email}' provided the following information: ${message} @@ -51,7 +54,7 @@ return job.stderr @web.expose - def report_error( self, trans, id, email="no email provided", message="" ): + def report_error( self, trans, id, email='', message="" ): smtp_server = trans.app.config.smtp_server if smtp_server is None: return trans.show_error_message( "Sorry, mail is not configured for this galaxy instance" ) @@ -61,9 +64,12 @@ # Get the dataset and associated job dataset = model.HistoryDatasetAssociation.get( id ) job = dataset.creating_job_associations[0].job + # Get the name of the server hosting the Galaxy instance from which this report originated + remote_hostname = trans.request.remote_hostname # Build the email message msg = MIMEText( string.Template( error_report_template ) - .safe_substitute( dataset_id=dataset.id, + .safe_substitute( remote_hostname=remote_hostname, + dataset_id=dataset.id, email=email, message=message, job_id=job.id, diff -r e899101e63d1 -r d83b9225b5dd lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Tue Jun 16 09:55:15 2009 -0400 +++ b/lib/galaxy/web/framework/base.py Tue Jun 16 13:54:33 2009 -0400 @@ -230,6 +230,12 @@ except socket.error: return self.remote_addr @lazy_property + def remote_hostname( self ): + try: + return socket.gethostbyaddr( self.remote_addr )[0] + except socket.error: + return self.remote_addr + @lazy_property def cookies( self ): return get_cookies( self.environ ) @lazy_property

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Re: [galaxy-dev] variable number of outputs
by Greg Von Kuster 18 Jun '09

18 Jun '09

Hello Len, This is not currently possible in a clean fashion, and providing this feature will take a bit longer than I had originally thought, so I've opened the following ticket for this. You can "follow" the issue in bitbucket if you want. Thanks for sending this. http://bitbucket.org/galaxy/galaxy-central/issue/97/enable-ability-to-have-… Greg Von Kuster Galaxy Development Team lentaing(a)jimmy.harvard.edu wrote: > Hi Greg, > > We have a program that can either output 1 (a bed file) or 2 files (a bed > and a wig file). We'd like to give the user the option to select whether > they want 1 or 2 files; in galaxy, is there a way to make the NUMBER of > outputs dependent on a variable? I tried this, but it didn't work--when i > select "False" for $two_out, galaxy still generates two output files: > > ... > <command interpreter="bash">test_cond_out.sh $output1 > </command> > <inputs> > <param name="two_out" type="select" display="radio"> > <option value="true">True</option> > <option value="false">False</option> > </param> > </inputs> > <outputs> > #if $two_out == "true": > <data format="bed" name="output1" /> > <data format="bed" name="output2" /> > #else: > <data format="bed" name="output1" /> > #end if > </outputs> > ... > > Thanks, > > Len > > >

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