{"version":"1.0","provider_name":"UCT HPC","provider_url":"https:\/\/ucthpc.uct.ac.za","author_name":"Andrew Lewis","author_url":"https:\/\/ucthpc.uct.ac.za\/index.php\/author\/andrew-lewis\/","title":"Velvet and BioPerl - UCT HPC","type":"rich","width":600,"height":338,"html":"<blockquote class=\"wp-embedded-content\" data-secret=\"MiFDfSRfvf\"><a href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/26\/velvet-and-bioperl\/\">Velvet and BioPerl<\/a><\/blockquote><iframe sandbox=\"allow-scripts\" security=\"restricted\" src=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/26\/velvet-and-bioperl\/embed\/#?secret=MiFDfSRfvf\" width=\"600\" height=\"338\" title=\"&#8220;Velvet and BioPerl&#8221; &#8212; UCT HPC\" data-secret=\"MiFDfSRfvf\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\" class=\"wp-embedded-content\"><\/iframe><script type=\"text\/javascript\">\n\/*! This file is auto-generated *\/\n!function(c,d){\"use strict\";var e=!1,o=!1;if(d.querySelector)if(c.addEventListener)e=!0;if(c.wp=c.wp||{},c.wp.receiveEmbedMessage);else if(c.wp.receiveEmbedMessage=function(e){var t=e.data;if(!t);else if(!(t.secret||t.message||t.value));else if(\/[^a-zA-Z0-9]\/.test(t.secret));else{for(var r,s,a,i=d.querySelectorAll('iframe[data-secret=\"'+t.secret+'\"]'),n=d.querySelectorAll('blockquote[data-secret=\"'+t.secret+'\"]'),o=new RegExp(\"^https?:$\",\"i\"),l=0;l<n.length;l++)n[l].style.display=\"none\";for(l=0;l<i.length;l++)if(r=i[l],e.source!==r.contentWindow);else{if(r.removeAttribute(\"style\"),\"height\"===t.message){if(1e3<(s=parseInt(t.value,10)))s=1e3;else if(~~s<200)s=200;r.height=s}if(\"link\"===t.message)if(s=d.createElement(\"a\"),a=d.createElement(\"a\"),s.href=r.getAttribute(\"src\"),a.href=t.value,!o.test(a.protocol));else if(a.host===s.host)if(d.activeElement===r)c.top.location.href=t.value}}},e)c.addEventListener(\"message\",c.wp.receiveEmbedMessage,!1),d.addEventListener(\"DOMContentLoaded\",t,!1),c.addEventListener(\"load\",t,!1);function t(){if(o);else{o=!0;for(var e,t,r,s=-1!==navigator.appVersion.indexOf(\"MSIE 10\"),a=!!navigator.userAgent.match(\/Trident.*rv:11\\.\/),i=d.querySelectorAll(\"iframe.wp-embedded-content\"),n=0;n<i.length;n++){if(!(r=(t=i[n]).getAttribute(\"data-secret\")))r=Math.random().toString(36).substr(2,10),t.src+=\"#?secret=\"+r,t.setAttribute(\"data-secret\",r);if(s||a)(e=t.cloneNode(!0)).removeAttribute(\"security\"),t.parentNode.replaceChild(e,t);t.contentWindow.postMessage({message:\"ready\",secret:r},\"*\")}}}}(window,document);\n<\/script>\n","description":"We recently ported Velvet, a short sequence assembler, to our cluster.&nbsp; It can be compiled with multi-threading via OMP, however there does not seem to be an elegant way to control its behaviour in a clustered environment other than to use PBS directives to book an entire node.&nbsp; The problem here is that a user would need a completely free node to start with.&nbsp; We'll see how well this works, however we may elect to recompile the application without OMP support.In addition to Velvet we installed the Velvet Optimiser.&nbsp; This is very simple to install, however one of the requirements is apparently BioPerl.&nbsp; This install was a bit more complex and required an install base directive to ensure that the scripts ended up in the NFS application mount.Velvet is memory hungry, on a node with 4GB of RAM an assembly took over an hour to reconstruct, whereas on a node with 24GB or RAM the same read took just over a minute.&nbsp; We're hoping that this application is swiftly ported to Grid format as our site has a distinct lack of large memory machines.","thumbnail_url":"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/assemble.png"}